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Sodium in PDB 3m1h: Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83

Protein crystallography data

The structure of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83, PDB code: 3m1h was solved by N.Li, C.A.Collyer, N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.24 / 1.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.251, 123.131, 62.614, 90.00, 91.25, 90.00
R / Rfree (%) 15.8 / 19.1

Other elements in 3m1h:

The structure of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 (pdb code 3m1h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83, PDB code: 3m1h:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3m1h

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Sodium binding site 1 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2003

b:20.0
occ:1.00
 O A:HOH695 2.1 28.0 1.0
O A:ASN1431 2.4 14.7 1.0
O A:HOH692 2.4 35.7 1.0
O A:HOH576 2.4 28.1 1.0
O A:HOH691 2.4 32.5 1.0
O A:HOH693 2.5 33.5 1.0
O A:HOH694 3.3 32.0 1.0
C A:ASN1431 3.5 16.8 1.0
O A:HOH574 4.3 29.8 1.0
CA A:GLU1432 4.3 13.8 1.0
OD1 A:ASN1431 4.3 19.2 1.0
N A:GLU1432 4.3 13.2 1.0
CB A:ASN1431 4.5 15.6 1.0
OE1 A:GLU1432 4.5 18.2 1.0
CA A:ASN1431 4.6 16.2 1.0
O A:HOH153 4.6 19.0 1.0
N A:ASP1433 4.6 13.0 1.0
CG A:ASN1431 4.6 17.6 1.0
OD2 A:ASP1433 4.7 22.2 1.0
CG A:ASP1433 4.7 15.3 1.0
OD1 A:ASP1433 4.8 17.8 1.0
C A:GLU1432 5.0 13.5 1.0

Sodium binding site 2 out of 9 in 3m1h

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Sodium binding site 2 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2004

b:16.2
occ:1.00
 O A:HOH682 2.3 32.8 1.0
O A:HOH460 2.3 29.6 1.0
OD1 A:ASN1530 2.4 16.3 1.0
O A:HOH163 2.4 22.6 1.0
O D:HOH327 2.5 28.5 1.0
O A:HOH604 2.6 30.2 1.0
O A:HOH366 2.6 23.7 1.0
CG A:ASN1530 3.4 16.5 1.0
O A:HOH215 3.5 30.0 1.0
ND2 A:ASN1530 3.9 16.1 1.0
NZ A:LYS1443 4.4 15.0 1.0
N A:ASN1530 4.4 15.8 1.0
OD1 A:ASP1531 4.6 16.4 1.0
O D:HOH603 4.6 30.1 1.0
OD2 A:ASP1531 4.6 15.3 1.0
CB A:ASN1530 4.7 13.4 1.0
O D:HOH222 4.9 19.3 1.0
CG A:ASP1531 4.9 14.0 1.0
O D:HOH71 4.9 23.8 1.0
OH A:TYR1578 4.9 25.2 1.0
CA A:ASN1530 5.0 12.7 1.0

Sodium binding site 3 out of 9 in 3m1h

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Sodium binding site 3 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2005

b:22.9
occ:1.00
 O A:HOH823 2.3 37.1 1.0
O A:HOH713 2.3 31.2 1.0
O A:HOH822 2.3 38.3 1.0
O A:TRP1442 2.3 15.6 1.0
O A:HOH259 2.4 21.3 1.0
O A:ALA1440 2.6 18.5 1.0
O A:HOH50 3.3 20.9 1.0
C A:ALA1440 3.5 15.3 1.0
C A:TRP1442 3.6 14.5 1.0
O A:HOH711 4.0 38.4 1.0
CA A:ALA1440 4.1 15.7 1.0
CA A:LYS1443 4.2 11.9 1.0
N A:LYS1443 4.3 12.1 1.0
N A:TRP1442 4.4 14.1 1.0
O A:PRO1439 4.6 15.1 1.0
N A:SER1441 4.6 15.5 1.0
C A:SER1441 4.6 13.6 1.0
O A:HOH437 4.6 27.5 1.0
CA A:TRP1442 4.7 14.1 1.0
O A:HOH698 4.7 34.5 1.0
CB A:LYS1443 4.7 13.3 1.0
O D:HOH412 4.8 23.0 1.0
CA A:SER1441 4.9 13.9 1.0
CB A:ALA1440 5.0 18.6 1.0

Sodium binding site 4 out of 9 in 3m1h

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Sodium binding site 4 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2003

b:20.4
occ:1.00
 O B:HOH688 2.3 32.3 1.0
O B:HOH686 2.3 35.3 1.0
O B:HOH689 2.3 31.5 1.0
O B:ASN1431 2.4 20.6 1.0
O B:HOH518 2.4 25.7 1.0
O B:HOH687 2.4 35.1 1.0
O B:HOH690 2.4 33.6 1.0
C B:ASN1431 3.5 15.3 1.0
OD1 B:ASN1431 4.2 21.8 1.0
N B:GLU1432 4.4 16.0 1.0
CA B:GLU1432 4.4 15.5 1.0
CB B:ASN1431 4.4 18.3 1.0
O B:HOH508 4.4 30.6 1.0
CG B:ASN1431 4.5 22.9 1.0
CA B:ASN1431 4.5 16.5 1.0
OD1 B:ASP1433 4.6 23.6 1.0
O B:HOH466 4.7 20.7 1.0
N B:ASP1433 4.7 16.6 1.0
OE1 B:GLU1432 4.7 22.0 1.0
CG B:ASP1433 4.7 23.8 1.0
OD2 B:ASP1433 4.9 21.8 1.0

Sodium binding site 5 out of 9 in 3m1h

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Sodium binding site 5 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2004

b:15.4
occ:1.00
 O B:HOH455 2.3 24.3 1.0
OD1 B:ASN1530 2.3 16.2 1.0
O B:HOH685 2.4 35.5 1.0
O B:HOH683 2.4 30.3 1.0
O C:HOH684 2.4 26.1 1.0
O B:HOH321 2.6 31.0 1.0
O B:HOH294 2.8 22.3 1.0
CG B:ASN1530 3.4 17.1 1.0
O B:HOH788 3.7 34.1 1.0
ND2 B:ASN1530 3.8 16.5 1.0
NZ B:LYS1443 4.4 13.9 1.0
O C:HOH115 4.4 30.2 1.0
N B:ASN1530 4.5 15.8 1.0
OD1 B:ASP1531 4.5 19.1 1.0
O C:HOH252 4.6 18.7 1.0
O C:HOH275 4.6 21.4 1.0
CB B:ASN1530 4.7 15.9 1.0
OD2 B:ASP1531 4.7 16.3 1.0
OH B:TYR1578 4.8 26.3 1.0
CG B:ASP1531 5.0 16.1 1.0
CA B:ASN1530 5.0 14.9 1.0

Sodium binding site 6 out of 9 in 3m1h

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Sodium binding site 6 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2005

b:21.8
occ:1.00
 O B:HOH825 2.3 36.4 1.0
O B:TRP1442 2.4 16.8 1.0
O B:HOH497 2.4 29.9 1.0
O B:HOH824 2.4 43.0 1.0
O B:HOH485 2.5 20.6 1.0
O B:ALA1440 2.6 16.2 1.0
O B:HOH365 3.3 23.3 1.0
C B:ALA1440 3.6 14.2 1.0
C B:TRP1442 3.6 14.9 1.0
CA B:ALA1440 4.0 15.4 1.0
CA B:LYS1443 4.3 12.1 1.0
N B:LYS1443 4.4 12.8 1.0
N B:TRP1442 4.5 15.1 1.0
O B:PRO1439 4.6 15.2 1.0
N B:SER1441 4.6 18.1 1.0
C B:SER1441 4.7 17.2 1.0
O B:HOH540 4.7 22.3 1.0
CA B:TRP1442 4.7 13.7 1.0
O C:HOH310 4.8 24.0 1.0
CB B:LYS1443 4.8 15.3 1.0
CB B:ALA1440 4.8 21.7 1.0

Sodium binding site 7 out of 9 in 3m1h

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Sodium binding site 7 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2003

b:12.4
occ:1.00
 O C:HOH516 2.3 27.0 1.0
O C:ASN1431 2.3 14.0 1.0
O C:HOH513 2.3 22.7 1.0
O C:HOH515 2.4 24.4 1.0
O C:HOH514 2.5 22.8 1.0
O C:HOH517 2.5 20.8 1.0
C C:ASN1431 3.6 12.9 1.0
CA C:GLU1432 4.4 14.3 1.0
N C:GLU1432 4.4 15.0 1.0
CB C:ASN1431 4.4 10.8 1.0
OE1 C:GLU1432 4.5 13.9 1.0
OD1 C:ASN1431 4.5 14.0 1.0
CA C:ASN1431 4.5 13.3 1.0
O C:HOH231 4.6 23.1 1.0
O C:HOH232 4.6 31.0 1.0
O D:HOH301 4.7 27.4 1.0
OD2 C:ASP1433 4.7 24.4 1.0
CG C:ASN1431 4.8 11.2 1.0
O D:HOH570 4.8 30.6 1.0
N C:ASP1433 4.9 12.2 1.0
CG C:ASP1433 4.9 16.5 1.0
O C:HOH628 5.0 27.5 1.0
OD1 C:ASP1433 5.0 16.1 1.0

Sodium binding site 8 out of 9 in 3m1h

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Sodium binding site 8 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2004

b:22.6
occ:1.00
 O C:HOH781 2.3 37.2 1.0
O C:HOH498 2.4 28.9 1.0
OE2 C:GLU1483 2.4 27.4 1.0
O C:HOH154 2.5 23.8 1.0
O C:HOH387 2.5 28.5 1.0
O B:HOH611 2.5 27.8 1.0
CD C:GLU1483 3.4 22.8 1.0
OE1 C:GLU1483 3.8 25.9 1.0
O C:HOH614 4.1 33.8 1.0
O C:HOH571 4.3 28.0 1.0
ND2 C:ASN1452 4.3 14.9 1.0
O C:HOH78 4.5 18.7 1.0
O C:ASP1450 4.6 15.3 1.0
CG C:GLU1483 4.6 22.6 1.0
CA B:GLY1451 4.7 14.6 1.0
O B:HOH519 4.8 30.7 1.0
NE2 C:GLN1486 4.8 13.1 1.0

Sodium binding site 9 out of 9 in 3m1h

Go back to Sodium Binding Sites List in 3m1h
Sodium binding site 9 out of 9 in the Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys- Gingipain (Kgp) From Porphyromonas Gingivalis W83 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2003

b:23.9
occ:1.00
 O D:HOH709 2.2 30.6 1.0
O D:HOH705 2.2 27.1 1.0
O A:HOH820 2.3 35.0 1.0
O A:HOH505 2.4 34.2 1.0
OE1 D:GLU1483 2.4 19.2 0.5
O D:HOH271 2.6 22.6 1.0
CD D:GLU1483 3.4 12.9 0.5
OE1 D:GLU1483 3.8 24.6 0.5
OE2 D:GLU1483 3.8 23.7 0.5
O D:HOH761 4.1 39.3 1.0
OD1 D:ASN1452 4.2 17.2 1.0
O D:HOH589 4.5 37.7 1.0
O D:HOH307 4.5 22.7 1.0
O D:ASP1450 4.6 13.0 1.0
CG D:GLU1483 4.6 10.9 0.5
CA A:GLY1451 4.7 14.4 1.0
O A:HOH590 4.7 36.1 1.0
NE2 D:GLN1486 4.8 12.3 1.0
CD D:GLU1483 4.8 22.4 0.5

Reference:

N.Li, P.Yun, C.M.Jeffries, D.Langley, R.Gamsjaeger, W.B.Church, N.Hunter, C.A.Collyer. The Modular Structure of Haemagglutinin/Adhesin Regions in Gingipains of Porphyromonas Gingivalis. Mol.Microbiol. V. 81 1358 2011.
ISSN: ISSN 0950-382X
PubMed: 21812842
DOI: 10.1111/J.1365-2958.2011.07768.X
Page generated: Mon Oct 7 11:25:37 2024

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