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Calcium 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:

Sodium (Na) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3m1h

Go back to Calcium Binding Sites List in 3m1h
Calcium binding site 1 out of 8 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 Calcium with other atoms in the Ca 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:Ca2001

b:13.6
occ:1.00
 OD1 A:ASP1446 2.3 15.7 1.0
OD1 A:ASN1490 2.4 13.1 1.0
O A:HOH211 2.4 14.4 1.0
O A:ASN1452 2.4 15.2 1.0
OD1 A:ASP1450 2.4 15.6 1.0
OD1 A:ASP1448 2.4 15.0 1.0
OD2 A:ASP1448 2.8 16.2 1.0
CG A:ASP1448 2.9 15.6 1.0
CG A:ASP1450 3.3 24.6 1.0
CG A:ASP1446 3.3 15.9 1.0
CG A:ASN1490 3.4 11.3 1.0
C A:ASN1452 3.5 11.3 1.0
OD2 A:ASP1450 3.8 18.1 1.0
ND2 A:ASN1490 3.8 11.8 1.0
OD2 A:ASP1446 4.0 16.9 1.0
N A:ASN1452 4.0 16.6 1.0
CA A:ASN1452 4.2 16.1 1.0
N A:ASP1450 4.2 16.2 1.0
CB A:ASN1452 4.3 17.1 1.0
CB A:ASP1446 4.4 13.2 1.0
CB A:ASP1448 4.4 17.4 1.0
CB A:ASP1450 4.5 17.8 1.0
CA A:ASP1446 4.5 10.3 1.0
N A:ASP1489 4.5 12.8 1.0
N A:GLY1449 4.6 13.6 1.0
O A:HOH159 4.6 14.7 1.0
N A:ASN1453 4.6 11.7 1.0
CA A:PRO1488 4.7 15.2 1.0
N A:GLY1451 4.7 14.8 1.0
CB A:ASN1490 4.7 12.2 1.0
N A:ASP1448 4.7 16.6 1.0
CA A:ASP1450 4.8 18.6 1.0
O A:ASP1489 4.8 13.4 1.0
C A:ASP1446 4.9 13.9 1.0
C A:ASP1489 4.9 14.8 1.0
CA A:ASN1453 4.9 10.8 1.0
CA A:ASP1448 5.0 15.9 1.0

Calcium binding site 2 out of 8 in 3m1h

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Calcium binding site 2 out of 8 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 Calcium with other atoms in the Ca 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:Ca2002

b:12.5
occ:1.00
 O A:ILE1472 2.3 12.6 1.0
OE2 A:GLU1435 2.3 17.1 1.0
O A:HOH10 2.4 14.4 1.0
O A:ASP1433 2.4 12.2 1.0
OD2 A:ASP1595 2.4 12.9 1.0
OD1 A:ASP1595 2.5 12.4 1.0
OG A:SER1470 2.5 14.6 1.0
CG A:ASP1595 2.8 10.6 1.0
CB A:SER1470 3.4 16.1 1.0
C A:ILE1472 3.5 11.7 1.0
CD A:GLU1435 3.5 20.3 1.0
C A:ASP1433 3.5 10.9 1.0
CG A:GLU1435 4.1 15.0 1.0
N A:ILE1472 4.2 14.6 1.0
CA A:ASP1433 4.2 12.0 1.0
CB A:ASP1433 4.2 14.8 1.0
CA A:ILE1472 4.3 16.1 1.0
CB A:ASP1595 4.4 10.5 1.0
OD1 A:ASP1596 4.4 15.6 1.0
N A:CYS1473 4.5 11.5 1.0
OE1 A:GLU1435 4.5 18.7 1.0
N A:PHE1434 4.6 12.6 1.0
O A:HOH164 4.6 28.1 1.0
O A:HIS1468 4.7 13.7 1.0
CA A:CYS1473 4.7 14.2 1.0
N A:HIS1468 4.7 13.2 1.0
CB A:ILE1472 4.7 16.4 1.0
CA A:SER1470 4.7 14.7 1.0
CB A:PHE1434 4.8 12.4 1.0
CA A:GLY1467 4.8 15.0 1.0
N A:GLU1435 4.8 13.1 1.0
C A:SER1470 4.9 14.9 1.0
C A:PHE1434 4.9 12.4 1.0
CA A:PHE1434 4.9 10.5 1.0

Calcium binding site 3 out of 8 in 3m1h

Go back to Calcium Binding Sites List in 3m1h
Calcium binding site 3 out of 8 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 Calcium with other atoms in the Ca 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
B:Ca2001

b:13.0
occ:1.00
 OD1 B:ASP1446 2.3 13.0 1.0
O B:ASN1452 2.4 12.8 1.0
OD1 B:ASP1448 2.4 14.6 1.0
OD1 B:ASN1490 2.4 11.4 1.0
OD1 B:ASP1450 2.4 13.4 1.0
O B:HOH18 2.4 15.0 1.0
OD2 B:ASP1448 2.8 14.6 1.0
CG B:ASP1448 2.9 13.5 1.0
CG B:ASP1450 3.3 18.5 1.0
CG B:ASP1446 3.4 14.0 1.0
CG B:ASN1490 3.4 9.6 1.0
C B:ASN1452 3.5 13.5 1.0
OD2 B:ASP1450 3.8 18.1 1.0
ND2 B:ASN1490 3.8 10.2 1.0
OD2 B:ASP1446 4.0 15.1 1.0
N B:ASN1452 4.0 13.6 1.0
CA B:ASN1452 4.2 14.3 1.0
N B:ASP1450 4.2 13.0 1.0
CB B:ASN1452 4.3 16.1 1.0
CB B:ASP1448 4.4 15.8 1.0
CB B:ASP1446 4.4 13.3 1.0
CB B:ASP1450 4.5 16.1 1.0
N B:GLY1449 4.5 16.0 1.0
CA B:ASP1446 4.5 10.3 1.0
O B:HOH158 4.6 12.9 1.0
N B:ASP1489 4.6 12.7 1.0
N B:ASN1453 4.6 12.1 1.0
N B:GLY1451 4.7 13.0 1.0
CA B:PRO1488 4.7 13.2 1.0
CA B:ASP1450 4.7 15.2 1.0
N B:ASP1448 4.8 16.3 1.0
CB B:ASN1490 4.8 9.4 1.0
C B:ASP1446 4.9 13.9 1.0
O B:ASP1489 4.9 12.6 1.0
CA B:ASN1453 4.9 12.8 1.0
CA B:ASP1448 5.0 15.7 1.0
C B:ASP1448 5.0 15.3 1.0

Calcium binding site 4 out of 8 in 3m1h

Go back to Calcium Binding Sites List in 3m1h
Calcium binding site 4 out of 8 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 Calcium with other atoms in the Ca 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:Ca2002

b:14.2
occ:1.00
 O B:ILE1472 2.3 13.7 1.0
O B:ASP1433 2.4 14.8 1.0
O B:HOH477 2.4 16.9 1.0
OE2 B:GLU1435 2.4 16.8 1.0
OD2 B:ASP1595 2.4 14.4 1.0
OD1 B:ASP1595 2.4 14.9 1.0
OG B:SER1470 2.6 15.1 1.0
CG B:ASP1595 2.8 17.6 1.0
C B:ASP1433 3.5 15.6 1.0
CB B:SER1470 3.5 18.5 1.0
C B:ILE1472 3.5 14.7 1.0
CD B:GLU1435 3.6 20.2 1.0
CA B:ASP1433 4.1 15.9 1.0
CG B:GLU1435 4.1 16.0 1.0
N B:ILE1472 4.2 17.4 1.0
CB B:ASP1433 4.2 16.0 1.0
OD1 B:ASP1596 4.2 19.1 1.0
CA B:ILE1472 4.3 16.2 1.0
CB B:ASP1595 4.3 11.6 1.0
N B:CYS1473 4.5 13.4 1.0
OE1 B:GLU1435 4.6 21.3 1.0
N B:PHE1434 4.6 14.3 1.0
O B:HOH478 4.7 27.6 1.0
O B:HIS1468 4.7 15.8 1.0
CA B:CYS1473 4.7 11.8 1.0
CB B:ILE1472 4.8 16.6 1.0
N B:HIS1468 4.8 14.0 1.0
CB B:PHE1434 4.8 13.5 1.0
CA B:SER1470 4.8 18.2 1.0
CA B:GLY1467 4.8 15.6 1.0
N B:GLU1435 4.9 17.1 1.0
C B:PHE1434 4.9 15.1 1.0
CA B:PHE1434 4.9 12.7 1.0
C B:SER1470 5.0 17.8 1.0

Calcium binding site 5 out of 8 in 3m1h

Go back to Calcium Binding Sites List in 3m1h
Calcium binding site 5 out of 8 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 Calcium with other atoms in the Ca 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
C:Ca2001

b:11.2
occ:1.00
 OD1 C:ASP1446 2.3 11.8 1.0
O C:ASN1452 2.3 12.0 1.0
OD1 C:ASP1448 2.3 11.4 1.0
O C:HOH100 2.4 12.2 1.0
OD1 C:ASN1490 2.4 11.2 1.0
OD1 C:ASP1450 2.4 11.7 1.0
OD2 C:ASP1448 2.9 12.1 1.0
CG C:ASP1448 3.0 12.4 1.0
CG C:ASP1450 3.3 16.9 1.0
CG C:ASP1446 3.4 15.0 1.0
CG C:ASN1490 3.4 9.1 1.0
C C:ASN1452 3.5 12.6 1.0
OD2 C:ASP1450 3.7 13.2 1.0
ND2 C:ASN1490 3.8 8.8 1.0
N C:ASN1452 4.0 11.7 1.0
CA C:ASN1452 4.1 12.6 1.0
OD2 C:ASP1446 4.1 11.9 1.0
CB C:ASN1452 4.2 10.6 1.0
N C:ASP1450 4.2 11.7 1.0
CB C:ASP1446 4.3 13.6 1.0
CA C:ASP1446 4.4 10.3 1.0
CB C:ASP1448 4.4 11.0 1.0
O C:HOH7 4.5 11.4 1.0
N C:GLY1449 4.5 10.7 1.0
N C:ASP1489 4.6 9.8 1.0
CB C:ASP1450 4.6 14.2 1.0
N C:ASN1453 4.6 12.2 1.0
CA C:PRO1488 4.6 12.4 1.0
N C:GLY1451 4.6 11.7 1.0
N C:ASP1448 4.7 10.7 1.0
C C:ASP1446 4.8 11.6 1.0
CB C:ASN1490 4.8 10.7 1.0
CA C:ASP1450 4.8 11.3 1.0
O C:ASP1489 4.9 12.5 1.0
CA C:ASN1453 5.0 8.7 1.0

Calcium binding site 6 out of 8 in 3m1h

Go back to Calcium Binding Sites List in 3m1h
Calcium binding site 6 out of 8 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 Calcium with other atoms in the Ca 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
C:Ca2002

b:11.2
occ:1.00
 O C:ILE1472 2.3 11.6 1.0
OE2 C:GLU1435 2.3 13.8 1.0
O C:ASP1433 2.4 12.2 1.0
OD2 C:ASP1595 2.4 11.6 1.0
O C:HOH36 2.4 14.8 1.0
OD1 C:ASP1595 2.5 11.4 1.0
OG C:SER1470 2.5 12.4 1.0
CG C:ASP1595 2.8 12.2 1.0
C C:ILE1472 3.5 11.0 1.0
CB C:SER1470 3.5 13.7 1.0
C C:ASP1433 3.5 10.8 1.0
CD C:GLU1435 3.5 18.2 1.0
CG C:GLU1435 4.1 13.1 1.0
N C:ILE1472 4.2 12.0 1.0
CA C:ASP1433 4.2 13.5 1.0
CB C:ASP1433 4.3 13.2 1.0
CA C:ILE1472 4.3 12.5 1.0
CB C:ASP1595 4.4 10.1 1.0
OD1 C:ASP1596 4.4 18.8 1.0
N C:CYS1473 4.5 10.9 1.0
OE1 C:GLU1435 4.6 16.5 1.0
N C:PHE1434 4.6 11.1 1.0
O C:HOH331 4.6 23.8 1.0
CA C:CYS1473 4.7 11.3 1.0
O C:HIS1468 4.7 14.3 1.0
N C:HIS1468 4.7 11.2 1.0
CB C:PHE1434 4.8 10.4 1.0
CA C:SER1470 4.8 13.4 1.0
CB C:ILE1472 4.8 14.3 1.0
N C:GLU1435 4.9 13.8 1.0
CA C:GLY1467 4.9 12.5 1.0
C C:SER1470 4.9 13.9 1.0
C C:PHE1434 4.9 12.2 1.0
CA C:PHE1434 4.9 10.3 1.0

Calcium binding site 7 out of 8 in 3m1h

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Calcium binding site 7 out of 8 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 Calcium with other atoms in the Ca 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
D:Ca2001

b:10.7
occ:1.00
 O D:ASN1452 2.3 11.2 1.0
OD1 D:ASP1446 2.3 11.3 1.0
OD1 D:ASP1448 2.4 12.5 1.0
OD1 D:ASP1450 2.4 11.6 1.0
OD1 D:ASN1490 2.4 10.2 1.0
O D:HOH28 2.4 10.8 1.0
OD2 D:ASP1448 2.8 12.9 1.0
CG D:ASP1448 2.9 13.0 1.0
CG D:ASP1450 3.3 11.3 1.0
CG D:ASP1446 3.4 11.0 1.0
CG D:ASN1490 3.4 8.5 1.0
C D:ASN1452 3.5 10.7 1.0
OD2 D:ASP1450 3.7 13.2 1.0
ND2 D:ASN1490 3.8 8.9 1.0
N D:ASN1452 4.0 13.1 1.0
CA D:ASN1452 4.1 12.0 1.0
OD2 D:ASP1446 4.1 12.1 1.0
CB D:ASN1452 4.1 10.2 1.0
N D:ASP1450 4.2 10.2 1.0
CB D:ASP1446 4.3 10.1 1.0
CB D:ASP1448 4.4 11.7 1.0
CA D:ASP1446 4.4 10.9 1.0
N D:GLY1449 4.5 11.5 1.0
CB D:ASP1450 4.5 12.0 1.0
O D:HOH37 4.5 11.5 1.0
N D:ASN1453 4.6 12.6 1.0
N D:ASP1489 4.6 10.8 1.0
CA D:PRO1488 4.6 12.9 1.0
N D:GLY1451 4.7 11.0 1.0
CA D:ASP1450 4.7 11.7 1.0
CB D:ASN1490 4.7 9.7 1.0
C D:ASP1446 4.8 11.8 1.0
N D:ASP1448 4.8 10.8 1.0
O D:ASP1489 4.9 11.3 1.0
CA D:ASN1453 4.9 10.8 1.0
CA D:ASP1448 5.0 10.2 1.0

Calcium binding site 8 out of 8 in 3m1h

Go back to Calcium Binding Sites List in 3m1h
Calcium binding site 8 out of 8 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 Calcium with other atoms in the Ca 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
D:Ca2002

b:13.7
occ:1.00
 O D:ILE1472 2.3 12.2 1.0
O D:HOH285 2.3 17.6 1.0
OE2 D:GLU1435 2.3 18.5 1.0
O D:ASP1433 2.4 13.9 1.0
OD2 D:ASP1595 2.4 11.5 1.0
OD1 D:ASP1595 2.5 13.8 1.0
OG D:SER1470 2.5 16.5 1.0
CG D:ASP1595 2.8 11.0 1.0
CB D:SER1470 3.5 17.1 1.0
C D:ILE1472 3.5 13.2 1.0
CD D:GLU1435 3.5 20.2 1.0
C D:ASP1433 3.6 13.8 1.0
CA D:ASP1433 4.1 13.4 1.0
CG D:GLU1435 4.2 13.9 1.0
N D:ILE1472 4.2 14.8 1.0
CB D:ASP1433 4.2 12.8 1.0
CA D:ILE1472 4.4 14.3 1.0
CB D:ASP1595 4.4 11.6 1.0
OD1 D:ASP1596 4.4 17.1 1.0
OE1 D:GLU1435 4.5 20.7 1.0
N D:CYS1473 4.5 12.7 1.0
O D:HOH24 4.6 25.2 1.0
N D:PHE1434 4.7 12.4 1.0
CA D:CYS1473 4.7 13.3 1.0
O D:HIS1468 4.7 18.8 1.0
N D:HIS1468 4.7 15.2 1.0
CA D:SER1470 4.8 15.5 1.0
CB D:ILE1472 4.8 13.9 1.0
N D:GLU1435 4.8 15.7 1.0
CA D:GLY1467 4.8 17.5 1.0
CB D:PHE1434 4.9 11.2 1.0
C D:SER1470 4.9 15.6 1.0
C D:PHE1434 5.0 14.1 1.0

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: Sat Jul 13 13:26:15 2024

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