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Calcium in PDB 7wss: Collagenase From Grimontia (Vibrio) Hollisae 1706B

Enzymatic activity of Collagenase From Grimontia (Vibrio) Hollisae 1706B

All present enzymatic activity of Collagenase From Grimontia (Vibrio) Hollisae 1706B:
3.4.24.3;

Protein crystallography data

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B, PDB code: 7wss was solved by T.Ikeuchi, M.Yasumoto, T.Takita, K.Mizutani, B.Mikami, K.Tanaka, S.Hattori, K.Yasukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.48 / 2.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.939, 75.12, 135.148, 90, 128.18, 90
R / Rfree (%) 18.6 / 22.7

Other elements in 7wss:

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Collagenase From Grimontia (Vibrio) Hollisae 1706B (pdb code 7wss). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Collagenase From Grimontia (Vibrio) Hollisae 1706B, PDB code: 7wss:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7wss

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Calcium binding site 1 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:30.2
occ:1.00
 O A:MET504 2.3 30.1 1.0
O A:HOH899 2.3 30.7 1.0
O A:GLY500 2.3 35.8 1.0
O A:GLY506 2.4 35.3 1.0
OE2 A:GLU461 2.4 39.6 1.0
O A:HOH832 2.4 29.2 1.0
CD A:GLU461 3.3 33.5 1.0
C A:GLY500 3.4 37.3 1.0
OE1 A:GLU461 3.4 35.1 1.0
C A:GLY506 3.5 39.0 1.0
C A:MET504 3.5 36.5 1.0
CA A:GLY500 3.8 34.3 1.0
N A:GLY506 3.8 36.3 1.0
C A:TYR505 3.9 31.0 1.0
O A:HOH850 4.1 38.2 1.0
O A:HOH812 4.1 27.1 1.0
O A:TYR505 4.2 37.5 1.0
CA A:GLY506 4.2 34.8 1.0
CB A:MET504 4.3 31.9 1.0
OD2 A:ASP425 4.3 30.5 1.0
N A:TYR505 4.4 38.6 1.0
CA A:TYR505 4.4 35.7 1.0
CA A:MET504 4.4 36.3 1.0
N A:ASP507 4.4 37.9 1.0
CG A:PRO464 4.5 30.7 1.0
N A:ARG501 4.5 36.2 1.0
O A:HOH889 4.6 33.3 1.0
CA A:ASP507 4.6 34.5 1.0
CG A:GLU461 4.7 35.1 1.0
CG2 A:VAL422 4.7 27.5 1.0
O A:ASP507 4.8 38.6 1.0
C A:ASP507 4.8 36.4 1.0
CA A:ARG501 4.8 33.6 1.0
N A:MET504 4.9 33.4 1.0
O A:HOH893 5.0 32.4 1.0

Calcium binding site 2 out of 8 in 7wss

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Calcium binding site 2 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:43.7
occ:1.00
 O A:HOH922 2.3 47.6 1.0
O A:ASP391 2.3 44.0 1.0
OE1 A:GLU477 2.3 42.1 1.0
OD1 A:ASN436 2.4 46.5 1.0
O A:HOH886 2.5 50.9 1.0
OE2 A:GLU477 2.6 39.1 1.0
O A:HOH838 2.6 45.5 1.0
CD A:GLU477 2.7 45.9 1.0
C A:ASP391 3.5 43.4 1.0
CG A:ASN436 3.6 49.2 1.0
CG A:GLU477 4.2 39.2 1.0
N A:MET392 4.3 43.0 1.0
CB A:ASP391 4.3 45.0 1.0
CA A:MET392 4.3 46.8 1.0
ND2 A:ASN436 4.4 35.9 1.0
OE1 A:GLN396 4.4 40.4 1.0
CA A:ASP391 4.5 45.5 1.0
CG A:ASP391 4.5 58.7 1.0
OD2 A:ASP391 4.6 52.7 1.0
O A:ASN436 4.6 40.0 1.0
NE2 A:GLN396 4.6 39.6 1.0
CB A:GLU477 4.6 36.6 1.0
CB A:ASN436 4.6 35.0 1.0
CA A:ASN436 4.6 41.1 1.0
O A:HOH815 4.7 38.4 1.0
CG A:MET392 4.9 46.1 1.0
CD A:GLN396 5.0 40.2 1.0

Calcium binding site 3 out of 8 in 7wss

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Calcium binding site 3 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:60.0
occ:1.00
 OG A:SER543 2.2 61.3 1.0
OG1 A:THR538 2.3 64.4 1.0
O A:HOH828 2.3 44.4 1.0
O A:SER543 2.5 53.6 1.0
OD1 A:ASP541 2.5 62.0 1.0
O A:THR538 2.6 63.0 1.0
OD2 A:ASP541 3.0 63.1 1.0
CG A:ASP541 3.1 65.2 1.0
CB A:THR538 3.4 58.5 1.0
CA A:THR538 3.4 59.3 1.0
C A:THR538 3.4 61.6 1.0
C A:SER543 3.4 58.7 1.0
CB A:SER543 3.5 58.5 1.0
CA A:SER543 3.8 62.8 1.0
N A:SER543 4.1 63.0 1.0
OD1 A:ASP561 4.2 60.3 1.0
OD2 A:ASP561 4.2 48.1 1.0
NE1 A:TRP566 4.3 56.8 1.0
CG2 A:THR538 4.4 56.6 1.0
CG A:ASP561 4.5 46.5 1.0
N A:THR544 4.6 60.4 1.0
CB A:ASP541 4.6 70.7 1.0
N A:ILE539 4.7 52.5 1.0
N A:THR538 4.8 60.6 1.0
CZ2 A:TRP566 4.9 58.5 1.0

Calcium binding site 4 out of 8 in 7wss

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Calcium binding site 4 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:75.0
occ:1.00
 O A:GLU173 2.2 64.4 1.0
O A:ILE179 2.6 55.9 1.0
O A:ASN176 2.7 62.1 1.0
C A:GLU173 3.4 60.6 1.0
C A:ASN176 3.7 67.2 1.0
C A:ILE179 3.8 58.2 1.0
CA A:SER177 4.1 71.2 1.0
CA A:GLU173 4.2 59.5 1.0
CG A:GLU173 4.2 49.2 1.0
OG1 A:THR180 4.2 50.7 1.0
O A:SER177 4.2 69.1 1.0
O A:PHE174 4.2 60.0 1.0
N A:SER177 4.3 69.5 1.0
C A:SER177 4.4 67.7 1.0
N A:PHE174 4.5 57.2 1.0
C A:PHE174 4.5 57.4 1.0
N A:ILE179 4.5 61.0 1.0
N A:ASN176 4.6 65.2 1.0
CA A:PHE174 4.6 60.0 1.0
CA A:ILE179 4.6 56.8 1.0
N A:THR180 4.7 51.7 1.0
CA A:ASN176 4.8 64.8 1.0
CB A:GLU173 4.8 54.5 1.0
CA A:THR180 4.8 57.1 1.0
O A:ALA172 4.9 58.5 1.0
CB A:ILE179 4.9 61.3 1.0

Calcium binding site 5 out of 8 in 7wss

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Calcium binding site 5 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:35.0
occ:1.00
 O B:GLY500 2.1 34.0 1.0
O B:MET504 2.2 33.0 1.0
O B:HOH882 2.3 27.5 1.0
OE2 B:GLU461 2.5 32.5 1.0
O B:GLY506 2.5 35.1 1.0
O B:HOH868 2.5 30.8 1.0
C B:GLY500 3.2 35.5 1.0
C B:MET504 3.4 31.8 1.0
CD B:GLU461 3.4 27.4 1.0
C B:GLY506 3.6 34.8 1.0
OE1 B:GLU461 3.7 35.3 1.0
CA B:GLY500 3.8 35.2 1.0
N B:GLY506 3.8 31.4 1.0
C B:TYR505 3.9 32.5 1.0
O B:HOH858 4.0 31.4 1.0
O B:HOH809 4.0 28.1 1.0
O B:TYR505 4.2 30.0 1.0
CA B:GLY506 4.3 27.8 1.0
OD2 B:ASP425 4.3 33.5 1.0
CB B:MET504 4.3 31.1 1.0
N B:TYR505 4.3 37.1 1.0
CA B:TYR505 4.3 29.1 1.0
N B:ARG501 4.4 33.2 1.0
CA B:MET504 4.4 35.7 1.0
CG B:PRO464 4.5 33.2 1.0
O B:HOH911 4.6 26.6 1.0
N B:ASP507 4.6 34.2 1.0
CG2 B:VAL422 4.7 25.4 1.0
CA B:ARG501 4.7 30.3 1.0
CA B:ASP507 4.8 38.0 1.0
CG B:GLU461 4.8 30.8 1.0
N B:MET504 4.9 33.6 1.0
O B:ASP507 4.9 42.2 1.0
C B:ASP507 5.0 38.5 1.0

Calcium binding site 6 out of 8 in 7wss

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Calcium binding site 6 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:42.7
occ:1.00
 O B:HOH943 2.2 40.9 1.0
OD1 B:ASN436 2.3 36.5 1.0
O B:HOH877 2.3 38.9 1.0
O B:ASP391 2.4 39.1 1.0
O B:HOH985 2.4 45.4 1.0
OE1 B:GLU477 2.6 39.6 1.0
OE2 B:GLU477 2.6 40.8 1.0
CD B:GLU477 2.9 42.1 1.0
C B:ASP391 3.5 34.5 1.0
CG B:ASN436 3.5 42.7 1.0
CB B:ASP391 4.2 37.0 1.0
CG B:GLU477 4.3 36.6 1.0
ND2 B:ASN436 4.4 27.7 1.0
OE1 B:GLN396 4.4 38.0 1.0
CG B:ASP391 4.4 53.3 1.0
OD2 B:ASP391 4.4 51.1 1.0
N B:MET392 4.4 33.4 1.0
CA B:ASP391 4.4 39.2 1.0
CA B:MET392 4.4 37.0 1.0
O B:ASN436 4.6 43.4 1.0
CB B:ASN436 4.6 36.4 1.0
O B:HOH821 4.6 34.7 1.0
CA B:ASN436 4.6 40.9 1.0
CB B:GLU477 4.7 40.6 1.0
NE2 B:GLN396 4.9 41.4 1.0

Calcium binding site 7 out of 8 in 7wss

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Calcium binding site 7 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:52.4
occ:1.00
 O B:HOH801 2.1 48.5 1.0
O B:THR538 2.2 39.0 1.0
OD1 B:ASP541 2.3 51.4 1.0
O B:SER543 2.4 50.4 1.0
OG B:SER543 2.4 47.6 1.0
OG1 B:THR538 2.6 50.4 1.0
O B:HOH848 2.8 41.1 1.0
OD2 B:ASP541 2.9 61.9 1.0
CG B:ASP541 3.0 60.7 1.0
C B:THR538 3.1 45.0 1.0
CA B:THR538 3.3 43.2 1.0
C B:SER543 3.4 51.8 1.0
CB B:THR538 3.5 45.3 1.0
CB B:SER543 3.6 47.3 1.0
CA B:SER543 3.8 56.2 1.0
N B:SER543 3.9 54.0 1.0
NE1 B:TRP566 4.4 43.5 1.0
N B:ILE539 4.4 46.8 1.0
CG2 B:THR538 4.4 42.0 1.0
CB B:ASP541 4.5 51.4 1.0
N B:THR544 4.5 58.5 1.0
OD1 B:ASP561 4.6 46.1 1.0
N B:THR538 4.7 43.6 1.0
CZ2 B:TRP566 4.7 47.4 1.0
OD2 B:ASP561 4.8 48.9 1.0
O B:ALA537 4.9 50.4 1.0
CE2 B:TRP566 4.9 47.2 1.0
CA B:ILE539 5.0 55.9 1.0

Calcium binding site 8 out of 8 in 7wss

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Calcium binding site 8 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:92.5
occ:1.00
 O B:GLU173 2.6 63.4 1.0
O B:HOH894 2.7 57.6 1.0
O B:ILE179 2.8 56.5 1.0
O B:ASN176 3.1 66.8 1.0
C B:GLU173 3.8 57.0 1.0
OG1 B:THR180 3.9 59.2 1.0
C B:ILE179 4.0 52.5 1.0
C B:ASN176 4.2 68.8 1.0
CG B:GLU173 4.3 52.6 1.0
O B:SER177 4.3 62.8 1.0
CA B:SER177 4.4 69.8 1.0
O B:PHE174 4.5 59.5 1.0
CA B:GLU173 4.6 51.7 1.0
C B:SER177 4.6 68.1 1.0
N B:SER177 4.7 66.0 1.0
CA B:THR180 4.7 48.5 1.0
N B:PHE174 4.7 57.7 1.0
C B:PHE174 4.8 54.6 1.0
N B:THR180 4.8 48.5 1.0
CA B:PHE174 4.8 53.6 1.0
N B:ILE179 4.9 59.1 1.0
CB B:THR180 4.9 61.7 1.0
CA B:ILE179 4.9 52.0 1.0

Reference:

T.Ikeuchi, M.Yasumoto, T.Takita, K.Tanaka, M.Kusubata, O.Hayashida, S.Hattori, K.Mizutani, B.Mikami, K.Yasukawa. Crystal Structure of Grimontia Hollisae Collagenase Provides Insights Into Its Novel Substrate Specificity Toward Collagen. J.Biol.Chem. V. 298 02109 2022.
ISSN: ESSN 1083-351X
PubMed: 35679897
DOI: 10.1016/J.JBC.2022.102109
Page generated: Fri Jul 19 05:52:51 2024

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