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Potassium in PDB 3irp: Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution, PDB code: 3irp was solved by Y.Tanaka, Y.Shouji, E.Matsuoka, M.Kuroda, I.Tanaka, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.18 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.935, 126.926, 45.830, 90.00, 96.75, 90.00
R / Rfree (%) 16.5 / 18.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution (pdb code 3irp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution, PDB code: 3irp:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 3irp

Go back to Potassium Binding Sites List in 3irp
Potassium binding site 1 out of 5 in the Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K1

b:8.6
occ:1.00
 O X:ASP775 2.4 13.0 1.0
O X:HOH29 2.4 8.1 1.0
OD1 X:ASP778 2.5 8.5 1.0
O X:HOH72 2.5 12.4 1.0
O X:HOH56 2.5 11.7 1.0
OD1 X:ASP780 2.5 9.8 1.0
OD2 X:ASP780 2.5 9.2 1.0
OD1 X:ASP775 2.6 12.6 1.0
CG X:ASP780 2.9 8.5 1.0
C X:ASP775 3.4 12.9 1.0
CG X:ASP775 3.5 14.2 1.0
CG X:ASP778 3.6 10.8 1.0
K X:K2 3.8 11.7 1.0
CA X:ASP775 4.0 13.2 1.0
OD2 X:ASP778 4.0 11.8 1.0
OD2 X:ASP775 4.1 17.1 1.0
O X:HOH264 4.2 33.1 1.0
CB X:ASP775 4.3 13.3 1.0
O X:ASP778 4.4 7.5 1.0
CB X:ASP780 4.4 8.2 1.0
O X:THR801 4.4 11.8 1.0
N X:ASP776 4.5 11.8 1.0
OD2 X:ASP803 4.5 7.9 1.0
CA X:ASP776 4.7 11.7 1.0
C X:ASP778 4.7 8.3 1.0
N X:ASP778 4.7 9.0 1.0
N X:ASP803 4.8 7.2 1.0
O X:HOH296 4.8 28.3 1.0
CB X:ASP778 4.8 9.2 1.0
CA X:ASP778 5.0 8.7 1.0
CG X:ASP803 5.0 8.3 1.0

Potassium binding site 2 out of 5 in 3irp

Go back to Potassium Binding Sites List in 3irp
Potassium binding site 2 out of 5 in the Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K2

b:11.7
occ:1.00
 OD1 X:ASP780 2.3 9.8 1.0
OD1 X:ASN771 2.4 15.4 1.0
O X:HOH200 2.4 19.7 1.0
OD1 X:ASP775 2.5 12.6 1.0
OD2 X:ASP778 2.5 11.8 1.0
O X:HOH296 2.6 28.3 1.0
O X:HOH352 2.7 28.1 1.0
CG X:ASP778 3.4 10.8 1.0
CG X:ASP775 3.5 14.2 1.0
CG X:ASN771 3.5 15.1 1.0
CG X:ASP780 3.6 8.5 1.0
OD1 X:ASP778 3.6 8.5 1.0
K X:K1 3.8 8.6 1.0
OD2 X:ASP775 4.1 17.1 1.0
CB X:ASP780 4.3 8.2 1.0
CB X:ASN771 4.3 14.8 1.0
CA X:ASP780 4.3 8.2 1.0
CA X:ASN771 4.4 14.4 1.0
O X:HOH56 4.4 11.7 1.0
O X:HOH387 4.5 30.7 1.0
OD2 X:ASP780 4.5 9.2 1.0
CB X:ASP775 4.5 13.3 1.0
ND2 X:ASN771 4.5 17.5 1.0
O X:SER779 4.6 8.8 1.0
CA X:ASP775 4.8 13.2 1.0
CB X:ASP778 4.8 9.2 1.0
O X:HOH203 4.8 23.0 1.0
N X:ASN771 4.9 14.0 1.0
N X:ASP780 5.0 8.0 1.0
C X:SER779 5.0 8.2 1.0

Potassium binding site 3 out of 5 in 3irp

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Potassium binding site 3 out of 5 in the Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K3

b:7.2
occ:1.00
 OD1 X:ASP705 2.3 9.2 1.0
OD1 X:ASN707 2.3 11.6 1.0
OD1 X:ASN713 2.3 9.2 1.0
OD2 X:ASP714 2.4 7.7 1.0
OD2 X:ASP709 2.5 10.7 1.0
O X:VAL711 2.5 7.4 1.0
OD1 X:ASP714 2.7 9.2 1.0
CG X:ASP714 2.9 9.0 1.0
CG X:ASN707 3.4 14.0 1.0
CG X:ASP709 3.4 11.5 1.0
CG X:ASP705 3.5 9.2 1.0
CG X:ASN713 3.5 8.9 1.0
C X:VAL711 3.6 8.0 1.0
OD1 X:ASP709 3.7 11.7 1.0
ND2 X:ASN707 3.9 15.2 1.0
N X:VAL711 4.0 9.1 1.0
N X:ASN713 4.0 7.9 1.0
ND2 X:ASN713 4.2 11.3 1.0
OD2 X:ASP705 4.2 10.6 1.0
CA X:VAL711 4.3 8.8 1.0
N X:ASP709 4.3 12.3 1.0
CB X:ASP714 4.4 8.7 1.0
N X:ASN707 4.4 11.9 1.0
C X:ASN713 4.4 8.4 1.0
NE1 X:TRP703 4.4 6.9 1.0
CB X:VAL711 4.4 9.1 1.0
CA X:ASP705 4.5 8.9 1.0
CB X:ASP705 4.5 8.8 1.0
CA X:ASN713 4.6 8.3 1.0
C X:ASP705 4.6 9.8 1.0
N X:ASP714 4.6 8.4 1.0
CB X:ASN707 4.6 12.5 1.0
CB X:ASP709 4.6 10.8 1.0
CB X:ASN713 4.6 8.2 1.0
N X:ASN708 4.7 13.3 1.0
N X:GLY710 4.7 9.5 1.0
O X:ASN713 4.7 8.7 1.0
N X:GLN712 4.7 8.0 1.0
N X:LYS706 4.8 10.5 1.0
CA X:ASN707 4.8 12.6 1.0
C X:ASN707 4.8 13.0 1.0
CA X:ASP709 4.8 11.0 1.0
O X:HOH61 5.0 13.1 1.0

Potassium binding site 4 out of 5 in 3irp

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Potassium binding site 4 out of 5 in the Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K4

b:11.6
occ:1.00
 O X:VAL496 2.6 8.8 1.0
O X:VAL440 2.6 7.0 1.0
O X:ASP438 2.6 6.8 1.0
OD1 X:ASP497 3.2 16.9 1.0
O X:HOH263 3.2 18.2 1.0
O X:HOH87 3.2 12.4 1.0
O X:HOH262 3.4 17.8 1.0
C X:VAL496 3.7 7.8 1.0
C X:ASP438 3.8 6.9 1.0
C X:VAL440 3.8 6.2 1.0
O X:HOH261 3.9 15.2 1.0
O X:HOH114 4.2 19.9 1.0
CA X:ASP497 4.3 9.3 1.0
CG X:ASP497 4.3 11.9 1.0
N X:ASP497 4.4 8.3 1.0
N X:VAL440 4.4 6.1 1.0
CA X:ASP438 4.5 6.5 1.0
CB X:VAL496 4.5 7.0 1.0
CG1 X:VAL441 4.6 8.0 1.0
CA X:VAL441 4.6 6.5 1.0
C X:SER439 4.6 6.8 1.0
N X:VAL441 4.6 6.3 1.0
CA X:VAL496 4.7 6.9 1.0
CG2 X:VAL496 4.7 7.5 1.0
CA X:VAL440 4.7 5.9 1.0
N X:SER439 4.7 6.4 1.0
CA X:SER439 4.9 6.7 1.0
CB X:ASP497 4.9 10.4 1.0

Potassium binding site 5 out of 5 in 3irp

Go back to Potassium Binding Sites List in 3irp
Potassium binding site 5 out of 5 in the Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Functional Region of Uafa From Staphylococcus Saprophyticus at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:K5

b:5.7
occ:1.00
 O X:ALA531 2.3 6.6 1.0
O X:VAL402 2.4 6.8 1.0
O X:ASN399 2.4 6.8 1.0
O X:HOH24 2.4 10.1 1.0
OE1 X:GLU533 2.4 8.2 1.0
O X:HOH111 2.5 11.9 1.0
OE2 X:GLU533 2.5 8.6 1.0
CD X:GLU533 2.8 8.0 1.0
C X:ALA531 3.5 7.0 1.0
C X:VAL402 3.5 6.7 1.0
C X:ASN399 3.5 6.2 1.0
CA X:PHE403 4.1 7.4 1.0
CB X:ALA531 4.2 6.9 1.0
N X:PHE403 4.3 6.9 1.0
CG X:GLU533 4.4 8.3 1.0
CA X:GLY532 4.4 7.1 1.0
N X:GLY532 4.4 6.9 1.0
N X:HIS400 4.4 6.7 1.0
N X:VAL402 4.4 6.4 1.0
N X:GLU533 4.4 7.7 1.0
CA X:ASN399 4.4 6.1 1.0
CA X:HIS400 4.5 7.1 1.0
O X:HOH942 4.5 30.0 1.0
CA X:ALA531 4.5 6.8 1.0
O X:HOH268 4.5 18.9 1.0
C X:GLY532 4.5 7.9 1.0
CA X:VAL402 4.6 6.2 1.0
O X:HOH90 4.6 16.1 1.0
C X:HIS400 4.7 7.4 1.0
CD1 X:PHE403 4.7 10.6 1.0
CB X:ASN399 4.8 6.0 1.0
O X:HOH331 4.8 26.1 1.0
N X:ALA404 4.9 7.9 1.0
O X:VAL530 5.0 6.4 1.0
CB X:PHE403 5.0 7.9 1.0

Reference:

E.Matsuoka, Y.Tanaka, M.Kuroda, Y.Shouji, T.Ohta, I.Tanaka, M.Yao. Crystal Structure of the Functional Region of Uro-Adherence Factor A From Staphylococcus Saprophyticus Reveals Participation of the B Domain in Ligand Binding Protein Sci. V. 20 406 2011.
ISSN: ISSN 0961-8368
PubMed: 21280131
DOI: 10.1002/PRO.573
Page generated: Mon Aug 12 08:34:30 2024

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