Atomistry » Calcium » PDB 3m0c-3mip » 3m1h
Atomistry »
  Calcium »
    PDB 3m0c-3mip »
      3m1h »

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

Go back to Calcium Binding Sites List in 3m1h
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

Go back to Calcium Binding Sites List in 3m1h
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 Dec 12 04:20:18 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy