Atomistry » Potassium » PDB 1pr9-1s61 » 1pvn
Atomistry »
  Potassium »
    PDB 1pr9-1s61 »
      1pvn »

Potassium in PDB 1pvn: The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp

Enzymatic activity of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp

All present enzymatic activity of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp:
1.1.1.205;

Protein crystallography data

The structure of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp, PDB code: 1pvn was solved by L.Gan, M.Seyedsayamdost, S.Shuto, A.Matsuda, G.A.Petsko, L.Hedstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.71 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.754, 112.566, 159.756, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.2

Potassium Binding Sites:

The binding sites of Potassium atom in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp (pdb code 1pvn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp, PDB code: 1pvn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 1 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K981

b:13.0
occ:1.00
 O D:GLY316 2.6 14.7 1.0
O D:GLY314 2.7 17.4 1.0
O A:GLU485 2.7 15.2 1.0
O D:CYS319 2.7 12.9 1.0
O A:GLY487 3.0 19.0 1.0
O A:GLY486 3.4 17.9 1.0
C A:GLY486 3.6 17.3 1.0
O A:HOH1034 3.7 19.9 1.0
C D:CYS319 3.7 13.8 1.0
C D:GLY316 3.7 14.5 1.0
C D:GLY314 3.8 16.0 1.0
C A:GLY487 3.8 19.1 1.0
C D:GLY315 3.8 15.5 1.0
C A:GLU485 3.8 15.0 1.0
CB D:CYS319 3.9 13.3 1.0
CD2 A:HIS489 4.0 15.8 1.0
N D:GLY316 4.0 14.8 1.0
O D:GLY315 4.0 13.8 1.0
CA A:GLY486 4.1 15.7 1.0
N A:GLY487 4.1 17.4 1.0
CA D:CYS319 4.1 14.0 1.0
N D:CYS319 4.1 13.0 1.0
NE2 A:HIS489 4.2 16.1 1.0
CA D:GLY315 4.2 14.9 1.0
CA A:GLY487 4.4 18.3 1.0
CA D:GLY316 4.4 14.7 1.0
N A:GLY486 4.4 14.9 1.0
N D:GLY315 4.4 15.6 1.0
N A:ALA488 4.6 19.0 1.0
N D:SER317 4.7 14.5 1.0
SG D:CYS319 4.7 16.8 1.0
N D:ILE320 4.8 13.1 1.0
CA A:ALA488 4.8 18.4 1.0
CA D:GLY314 4.8 15.7 1.0
C D:SER317 4.8 15.7 1.0
O D:SER317 4.9 18.3 1.0
CA D:SER317 4.9 15.7 1.0

Potassium binding site 2 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 2 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K987

b:18.0
occ:1.00
 O B:GLY20 2.5 16.1 1.0
OD2 A:ASP264 2.6 21.8 1.0
OG B:SER22 2.6 19.6 1.0
O B:ASN460 2.7 16.3 1.0
O A:PHE266 2.7 12.9 1.0
OD1 A:ASP264 3.0 15.1 1.0
CG A:ASP264 3.2 17.6 1.0
CB B:SER22 3.6 18.9 1.0
N B:SER22 3.6 16.8 1.0
O A:HOH1079 3.6 27.9 1.0
C B:GLY20 3.7 16.4 1.0
C B:ASN460 3.7 18.2 1.0
C A:PHE266 3.7 15.9 1.0
CB A:PHE266 3.8 14.2 1.0
CB B:PRO19 4.0 17.3 1.0
CA B:ASN460 4.1 17.4 1.0
C B:LEU21 4.1 17.6 1.0
CA B:SER22 4.1 18.1 1.0
N B:GLY20 4.2 18.1 1.0
CA A:PHE266 4.2 14.7 1.0
CA B:LEU21 4.3 18.0 1.0
N B:LEU21 4.5 18.0 1.0
N A:PHE266 4.5 14.9 1.0
C B:PRO19 4.6 17.2 1.0
CG A:PHE266 4.6 16.0 1.0
CB A:ASP264 4.6 15.8 1.0
CA B:GLY20 4.6 17.2 1.0
CA B:PRO19 4.7 17.2 1.0
O B:CYS459 4.7 14.6 1.0
CB B:ASN460 4.7 17.7 1.0
N A:SER267 4.8 16.5 1.0
O B:LEU21 4.9 16.2 1.0
N B:CYS461 4.9 18.0 1.0
O A:HOH1047 4.9 14.7 1.0
CB A:SER267 5.0 20.6 1.0

Potassium binding site 3 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 3 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K988

b:16.1
occ:1.00
 O A:GLY20 2.4 14.4 1.0
OD2 D:ASP264 2.5 23.5 1.0
OG A:SER22 2.5 17.8 1.0
O A:ASN460 2.6 14.1 1.0
O D:PHE266 2.8 15.7 1.0
OD1 D:ASP264 3.1 20.1 1.0
CG D:ASP264 3.2 20.5 1.0
CB A:SER22 3.5 15.7 1.0
N A:SER22 3.5 16.3 1.0
C A:GLY20 3.6 14.8 1.0
O D:HOH1202 3.6 23.9 1.0
C A:ASN460 3.6 17.1 1.0
C D:PHE266 3.8 17.1 1.0
CB D:PHE266 3.9 14.3 1.0
C A:LEU21 4.0 17.0 1.0
CB A:PRO19 4.0 16.7 1.0
CA A:ASN460 4.0 15.8 1.0
CA A:SER22 4.0 18.1 1.0
N A:GLY20 4.2 15.2 1.0
CA A:LEU21 4.3 16.2 1.0
CA D:PHE266 4.3 15.6 1.0
N A:LEU21 4.4 15.6 1.0
C A:PRO19 4.6 15.4 1.0
N D:PHE266 4.6 16.7 1.0
CA A:GLY20 4.6 14.8 1.0
CB D:ASP264 4.6 16.9 1.0
O A:CYS459 4.6 13.9 1.0
CG D:PHE266 4.7 14.8 1.0
CB A:ASN460 4.7 15.7 1.0
CA A:PRO19 4.8 15.5 1.0
O A:LEU21 4.8 16.0 1.0
N A:CYS461 4.8 17.0 1.0
N D:SER267 4.9 16.0 1.0
O D:HOH1002 4.9 10.8 1.0

Potassium binding site 4 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 4 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K982

b:15.4
occ:1.00
 O A:GLY316 2.6 13.6 1.0
O A:CYS319 2.6 16.4 1.0
O B:GLY487 2.6 20.2 1.0
O A:GLY314 2.7 17.9 1.0
O B:GLU485 2.7 19.8 1.0
O B:GLY486 2.9 21.4 1.0
C B:GLY486 3.1 21.2 1.0
C B:GLY487 3.3 21.1 1.0
N B:GLY487 3.6 21.7 1.0
C A:CYS319 3.6 17.4 1.0
O B:HOH1004 3.7 24.2 1.0
C A:GLY316 3.7 13.4 1.0
C B:GLU485 3.8 19.0 1.0
CA B:GLY486 3.8 19.7 1.0
C A:GLY314 3.8 16.6 1.0
CA B:GLY487 3.8 21.9 1.0
CB A:CYS319 3.9 17.5 1.0
C A:GLY315 3.9 14.9 1.0
N A:GLY316 4.0 12.8 1.0
CA A:CYS319 4.1 18.0 1.0
O A:GLY315 4.1 15.2 1.0
N A:CYS319 4.1 17.1 1.0
CD2 B:HIS489 4.1 17.4 1.0
N B:ALA488 4.1 21.0 1.0
N B:GLY486 4.2 18.2 1.0
CA A:GLY315 4.3 15.3 1.0
CA A:GLY316 4.4 13.6 1.0
N A:GLY315 4.5 15.8 1.0
CA B:ALA488 4.5 21.0 1.0
NE2 B:HIS489 4.5 16.7 1.0
SG A:CYS319 4.7 19.5 1.0
N A:SER317 4.7 14.8 1.0
N A:ILE320 4.7 15.8 1.0
CA A:GLY314 4.8 17.2 1.0
C A:SER317 4.8 16.3 1.0
O A:SER317 4.9 16.2 1.0
CA A:SER317 4.9 16.3 1.0

Potassium binding site 5 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 5 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K986

b:19.3
occ:1.00
 O C:GLY20 2.4 16.7 1.0
OG C:SER22 2.5 21.8 1.0
OD2 B:ASP264 2.5 24.4 1.0
O C:ASN460 2.5 16.1 1.0
O B:PHE266 2.7 13.8 1.0
OD1 B:ASP264 3.0 19.9 1.0
CG B:ASP264 3.1 21.2 1.0
O B:HOH1027 3.4 26.0 1.0
CB C:SER22 3.5 20.3 1.0
N C:SER22 3.5 18.9 1.0
C C:ASN460 3.5 17.2 1.0
C C:GLY20 3.6 16.3 1.0
C B:PHE266 3.7 14.9 1.0
CB B:PHE266 3.7 15.0 1.0
CA C:ASN460 3.9 17.0 1.0
CB C:PRO19 4.0 18.1 1.0
CA C:SER22 4.0 19.6 1.0
C C:LEU21 4.0 19.4 1.0
N C:GLY20 4.2 17.0 1.0
CA B:PHE266 4.2 14.6 1.0
CA C:LEU21 4.3 18.6 1.0
N C:LEU21 4.4 16.7 1.0
N B:PHE266 4.5 14.3 1.0
O C:CYS459 4.6 16.5 1.0
CG B:PHE266 4.6 16.1 1.0
C C:PRO19 4.6 17.0 1.0
CB B:ASP264 4.6 18.5 1.0
CA C:GLY20 4.6 16.5 1.0
CB C:ASN460 4.7 17.2 1.0
CA C:PRO19 4.7 17.3 1.0
N C:CYS461 4.7 16.5 1.0
O C:LEU21 4.8 19.7 1.0
N B:SER267 4.8 14.6 1.0
O B:HOH1003 4.9 14.9 1.0

Potassium binding site 6 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 6 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K984

b:17.2
occ:1.00
 OG D:SER22 2.5 17.3 1.0
OD2 C:ASP264 2.5 20.3 1.0
O D:GLY20 2.6 17.6 1.0
O D:ASN460 2.6 17.1 1.0
O C:PHE266 2.8 12.7 1.0
OD1 C:ASP264 3.1 17.6 1.0
CG C:ASP264 3.2 18.9 1.0
CB D:SER22 3.5 19.2 1.0
C D:ASN460 3.6 18.4 1.0
N D:SER22 3.7 17.9 1.0
O C:HOH1052 3.7 25.4 1.0
C C:PHE266 3.8 16.6 1.0
C D:GLY20 3.8 17.4 1.0
CB C:PHE266 3.9 13.4 1.0
CA D:ASN460 3.9 18.4 1.0
CB D:PRO19 4.0 16.4 1.0
CA D:SER22 4.1 19.4 1.0
C D:LEU21 4.2 16.8 1.0
N D:GLY20 4.3 17.2 1.0
CA C:PHE266 4.3 15.1 1.0
CA D:LEU21 4.5 16.8 1.0
N C:PHE266 4.6 15.8 1.0
N D:LEU21 4.6 17.3 1.0
CB D:ASN460 4.6 19.3 1.0
O D:CYS459 4.6 18.1 1.0
CB C:ASP264 4.6 16.4 1.0
CG C:PHE266 4.7 15.6 1.0
C D:PRO19 4.7 16.5 1.0
CA D:PRO19 4.8 16.2 1.0
CA D:GLY20 4.8 17.7 1.0
N D:CYS461 4.8 16.1 1.0
N C:SER267 4.9 15.8 1.0
ND2 D:ASN460 4.9 21.6 1.0
O C:HOH1023 4.9 15.9 1.0
O D:LEU21 5.0 16.3 1.0

Potassium binding site 7 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 7 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K985

b:17.9
occ:1.00
 O C:GLU485 2.6 16.0 1.0
O B:GLY316 2.6 14.4 1.0
O B:GLY314 2.6 20.3 1.0
O B:CYS319 2.7 15.9 1.0
O C:GLY487 2.9 19.2 1.0
O C:GLY486 3.1 19.4 1.0
C C:GLY486 3.3 18.7 1.0
C C:GLY487 3.6 19.6 1.0
O C:HOH1029 3.6 20.8 1.0
C B:CYS319 3.7 16.8 1.0
C C:GLU485 3.7 16.7 1.0
C B:GLY316 3.7 17.3 1.0
C B:GLY314 3.7 17.4 1.0
CA C:GLY486 3.8 17.1 1.0
N C:GLY487 3.8 18.9 1.0
C B:GLY315 3.9 17.9 1.0
CB B:CYS319 3.9 16.6 1.0
N B:GLY316 4.0 17.4 1.0
CD2 C:HIS489 4.0 15.3 1.0
O B:GLY315 4.0 17.4 1.0
CA B:CYS319 4.1 16.6 1.0
N B:CYS319 4.2 15.6 1.0
CA C:GLY487 4.2 18.8 1.0
N C:GLY486 4.2 16.2 1.0
CA B:GLY315 4.2 17.6 1.0
NE2 C:HIS489 4.3 16.5 1.0
CA B:GLY316 4.4 16.0 1.0
N B:GLY315 4.4 18.3 1.0
N C:ALA488 4.5 19.8 1.0
SG B:CYS319 4.7 18.9 1.0
N B:SER317 4.7 15.3 1.0
CA B:GLY314 4.8 18.6 1.0
N B:ILE320 4.8 16.2 1.0
CA C:ALA488 4.8 19.3 1.0
C B:SER317 4.9 16.8 1.0
O B:SER317 4.9 18.3 1.0
CA C:GLU485 4.9 17.0 1.0
CA B:SER317 4.9 17.8 1.0

Potassium binding site 8 out of 8 in 1pvn

Go back to Potassium Binding Sites List in 1pvn
Potassium binding site 8 out of 8 in the The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of The Crystal Structure of the Complex Between Imp Dehydrogenase Catalytic Domain and A Transition State Analogue Mzp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K983

b:14.1
occ:1.00
 O C:GLY316 2.6 12.5 1.0
O D:GLU485 2.6 17.6 1.0
O C:CYS319 2.7 12.3 1.0
O D:GLY487 2.7 19.9 1.0
O C:GLY314 2.7 17.4 1.0
O D:GLY486 3.1 19.7 1.0
C D:GLY486 3.3 19.4 1.0
C D:GLY487 3.4 18.9 1.0
C C:CYS319 3.6 14.1 1.0
C C:GLY316 3.7 14.4 1.0
N D:GLY487 3.7 19.8 1.0
O D:HOH1009 3.7 18.8 1.0
C D:GLU485 3.7 18.2 1.0
C C:GLY314 3.8 17.3 1.0
C C:GLY315 3.9 15.7 1.0
CA D:GLY486 3.9 18.7 1.0
CB C:CYS319 3.9 14.1 1.0
CD2 D:HIS489 4.0 17.0 1.0
CA D:GLY487 4.0 19.9 1.0
N C:GLY316 4.0 14.4 1.0
O C:GLY315 4.0 14.6 1.0
CA C:CYS319 4.1 13.2 1.0
N C:CYS319 4.1 14.2 1.0
N D:ALA488 4.2 18.0 1.0
N D:GLY486 4.3 17.6 1.0
CA C:GLY315 4.3 15.0 1.0
NE2 D:HIS489 4.3 17.4 1.0
CA C:GLY316 4.4 13.6 1.0
N C:GLY315 4.5 16.1 1.0
CA D:ALA488 4.5 18.0 1.0
SG C:CYS319 4.6 19.1 1.0
N C:SER317 4.7 14.8 1.0
N C:ILE320 4.8 14.3 1.0
C C:SER317 4.8 16.3 1.0
O C:SER317 4.8 16.9 1.0
CA C:GLY314 4.8 17.4 1.0
CA C:SER317 4.9 15.2 1.0
CA D:GLU485 5.0 17.4 1.0
O D:HOH1220 5.0 45.4 1.0

Reference:

L.Gan, M.Seyedsayamdost, S.Shuto, A.Matsuda, G.A.Petsko, L.Hedstrom. The Immunosuppressive Agent Mizoribine Monophosphate Forms A Transition State Analogue Complex with Inosine Monophosphate Dehydrogenase Biochemistry V. 42 857 2003.
ISSN: ISSN 0006-2960
PubMed: 12549902
DOI: 10.1021/BI0271401
Page generated: Mon Aug 12 05:13:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy