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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

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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

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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

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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

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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

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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

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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

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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

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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

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