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Calcium in PDB 7xeb: Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp

Enzymatic activity of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp

All present enzymatic activity of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp:
3.4.24.3;

Protein crystallography data

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp, PDB code: 7xeb 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) 45.41 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.972, 75.549, 130.551, 90, 103.06, 90
R / Rfree (%) 20.6 / 25.5

Other elements in 7xeb:

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp 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 Complexed with Gly- Pro-Hyp (pdb code 7xeb). 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 Complexed with Gly- Pro-Hyp, PDB code: 7xeb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7xeb

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Calcium binding site 1 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:30.8
occ:1.00
 O A:HOH848 2.2 26.4 1.0
O A:MET504 2.2 34.4 1.0
O A:GLY500 2.3 35.3 1.0
OE2 A:GLU461 2.3 37.2 1.0
O A:GLY506 2.4 32.9 1.0
O A:HOH813 2.5 29.6 1.0
CD A:GLU461 3.3 39.5 1.0
C A:GLY500 3.4 35.3 1.0
C A:MET504 3.5 36.8 1.0
C A:GLY506 3.5 30.1 1.0
OE1 A:GLU461 3.6 36.9 1.0
N A:GLY506 3.8 28.5 1.0
C A:TYR505 3.9 30.9 1.0
CA A:GLY500 3.9 34.5 1.0
OD2 A:ASP425 4.1 35.4 1.0
O A:HOH820 4.1 33.4 1.0
O A:TYR505 4.2 36.8 1.0
CA A:GLY506 4.2 29.1 1.0
CB A:MET504 4.3 34.5 1.0
O A:HOH810 4.3 32.2 1.0
N A:TYR505 4.3 30.7 1.0
CA A:TYR505 4.4 35.2 1.0
CG A:PRO464 4.4 30.5 1.0
CA A:MET504 4.4 33.3 1.0
N A:ASP507 4.5 29.7 1.0
N A:ARG501 4.5 31.9 1.0
CG2 A:VAL422 4.6 30.1 1.0
CA A:ASP507 4.7 28.5 1.0
O A:HOH875 4.7 32.8 1.0
CG A:GLU461 4.7 31.3 1.0
O A:ASP507 4.8 31.2 1.0
CA A:ARG501 4.8 31.1 1.0
N A:MET504 4.9 33.2 1.0
C A:ASP507 4.9 33.0 1.0

Calcium binding site 2 out of 8 in 7xeb

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Calcium binding site 2 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:41.4
occ:1.00
 O A:HOH857 2.2 40.2 1.0
OE1 A:GLU477 2.4 32.5 1.0
OD1 A:ASN436 2.4 36.6 1.0
O A:HOH879 2.5 34.6 1.0
O A:ASP391 2.5 30.4 1.0
OE2 A:GLU477 2.6 35.4 1.0
CD A:GLU477 2.8 32.4 1.0
CG A:ASN436 3.3 39.1 1.0
C A:ASP391 3.7 37.7 1.0
ND2 A:ASN436 3.8 46.6 1.0
CG A:GLU477 4.3 35.2 1.0
CB A:ASP391 4.4 32.5 1.0
CB A:ASN436 4.4 31.4 1.0
OD2 A:ASP391 4.4 50.6 1.0
OE1 A:GLN396 4.5 37.5 1.0
O A:ASN436 4.5 32.6 1.0
CG A:ASP391 4.6 43.8 1.0
CA A:ASN436 4.6 32.9 1.0
N A:MET392 4.6 39.7 1.0
CA A:ASP391 4.6 40.8 1.0
CA A:MET392 4.6 40.5 1.0
O A:HOH817 4.7 31.1 1.0
CB A:GLU477 4.7 27.2 1.0
NE2 A:GLN396 4.7 35.7 1.0

Calcium binding site 3 out of 8 in 7xeb

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Calcium binding site 3 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:53.3
occ:1.00
 OG A:SER543 2.3 56.9 1.0
O A:SER543 2.3 60.4 1.0
OG1 A:THR538 2.4 59.7 1.0
OD1 A:ASP541 2.5 60.3 1.0
O A:THR538 2.6 60.6 1.0
OD2 A:ASP541 2.7 63.4 1.0
CG A:ASP541 2.9 60.6 1.0
C A:SER543 3.4 56.2 1.0
C A:THR538 3.4 57.5 1.0
CA A:THR538 3.5 51.6 1.0
CB A:THR538 3.5 50.4 1.0
CB A:SER543 3.5 54.8 1.0
CA A:SER543 3.8 57.8 1.0
N A:SER543 4.1 55.0 1.0
OD2 A:ASP561 4.2 42.5 1.0
CG2 A:THR538 4.3 42.8 1.0
NE1 A:TRP566 4.4 42.9 1.0
CB A:ASP541 4.5 58.3 1.0
N A:THR544 4.5 51.3 1.0
OD1 A:ASP561 4.5 55.7 1.0
N A:ILE539 4.7 57.1 1.0
CG A:ASP561 4.7 38.2 1.0
CZ2 A:TRP566 4.9 41.9 1.0
N A:THR538 4.9 56.4 1.0
CA A:THR544 4.9 48.7 1.0

Calcium binding site 4 out of 8 in 7xeb

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Calcium binding site 4 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:71.9
occ:1.00
 O A:ILE179 2.3 60.8 1.0
O A:GLU173 2.3 51.7 1.0
O A:ASN176 2.4 59.4 1.0
C A:ILE179 3.4 57.9 1.0
C A:GLU173 3.5 53.2 1.0
C A:ASN176 3.5 57.4 1.0
CA A:SER177 3.8 60.3 1.0
N A:ILE179 4.0 59.9 1.0
C A:SER177 4.0 59.9 1.0
O A:SER177 4.0 62.3 1.0
CA A:GLU173 4.1 50.4 1.0
N A:SER177 4.1 64.6 1.0
CG A:GLU173 4.1 48.9 1.0
CA A:ILE179 4.1 56.6 1.0
OG1 A:THR180 4.3 54.7 1.0
CB A:ILE179 4.4 57.1 1.0
N A:THR180 4.5 55.8 1.0
N A:PHE174 4.6 54.1 1.0
N A:ASN176 4.6 53.2 1.0
CA A:ASN176 4.7 52.8 1.0
CA A:THR180 4.7 53.7 1.0
CB A:GLU173 4.8 47.7 1.0
O A:ALA172 4.8 46.3 1.0
N A:ASN178 4.8 61.2 1.0
O A:PHE174 4.8 59.0 1.0
C A:PHE174 4.8 55.1 1.0
CA A:PHE174 4.8 48.1 1.0

Calcium binding site 5 out of 8 in 7xeb

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Calcium binding site 5 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:37.5
occ:1.00
 O B:GLY500 2.2 38.9 1.0
O B:MET504 2.2 37.6 1.0
OE2 B:GLU461 2.2 35.7 1.0
O B:HOH823 2.3 33.1 1.0
O B:GLY506 2.4 45.5 1.0
O B:HOH809 2.5 36.5 1.0
CD B:GLU461 3.3 37.6 1.0
C B:GLY500 3.3 42.6 1.0
C B:MET504 3.4 44.6 1.0
C B:GLY506 3.5 34.9 1.0
OE1 B:GLU461 3.6 43.6 1.0
N B:GLY506 3.9 38.2 1.0
C B:TYR505 3.9 42.9 1.0
CA B:GLY500 3.9 40.5 1.0
O B:HOH803 4.1 38.9 1.0
O B:HOH802 4.1 33.6 1.0
O B:TYR505 4.2 45.3 1.0
CB B:MET504 4.2 40.5 1.0
OD2 B:ASP425 4.3 42.3 1.0
CA B:GLY506 4.3 39.0 1.0
N B:TYR505 4.3 46.4 1.0
CA B:TYR505 4.3 45.8 1.0
CA B:MET504 4.3 39.6 1.0
N B:ARG501 4.4 33.1 1.0
CG B:PRO464 4.5 42.8 1.0
N B:ASP507 4.5 32.8 1.0
O B:HOH824 4.5 43.3 1.0
CG B:GLU461 4.6 38.5 1.0
CG2 B:VAL422 4.6 32.0 1.0
CA B:ASP507 4.7 38.0 1.0
O B:ASP507 4.7 38.7 1.0
CA B:ARG501 4.7 33.7 1.0
N B:MET504 4.8 43.8 1.0
C B:ASP507 4.9 40.6 1.0
O B:HOH813 5.0 40.3 1.0

Calcium binding site 6 out of 8 in 7xeb

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Calcium binding site 6 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:55.9
occ:1.00
 OE1 B:GLU477 2.4 48.2 1.0
OE2 B:GLU477 2.5 45.0 1.0
O B:ASP391 2.5 49.7 1.0
OD1 B:ASN436 2.6 52.2 1.0
O B:HOH804 2.6 49.9 1.0
CD B:GLU477 2.7 49.5 1.0
CG B:ASN436 3.5 53.8 1.0
C B:ASP391 3.7 48.7 1.0
ND2 B:ASN436 4.0 55.9 1.0
CG B:GLU477 4.2 41.3 1.0
OD2 B:ASP391 4.2 62.9 1.0
CB B:ASP391 4.3 46.0 1.0
CG B:ASP391 4.4 62.5 1.0
O B:ASN436 4.4 54.3 1.0
CB B:ASN436 4.5 51.7 1.0
CA B:ASN436 4.5 51.9 1.0
O B:HOH819 4.6 44.4 1.0
CA B:ASP391 4.6 50.9 1.0
CB B:GLU477 4.6 44.3 1.0
N B:MET392 4.7 43.1 1.0
CA B:MET392 4.7 44.7 1.0
OE1 B:GLN396 4.7 34.5 1.0

Calcium binding site 7 out of 8 in 7xeb

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Calcium binding site 7 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:60.7
occ:1.00
 OG B:SER543 2.4 60.7 1.0
OD2 B:ASP541 2.5 80.8 1.0
OG1 B:THR538 2.6 58.7 1.0
O B:SER543 2.6 65.0 1.0
OD1 B:ASP541 2.7 78.0 1.0
O B:THR538 2.9 67.7 1.0
CG B:ASP541 2.9 79.4 1.0
C B:SER543 3.6 65.0 1.0
CB B:SER543 3.6 63.6 1.0
CA B:THR538 3.7 68.2 1.0
CB B:THR538 3.7 66.2 1.0
C B:THR538 3.7 68.7 1.0
OD2 B:ASP561 4.0 50.9 1.0
CA B:SER543 4.0 68.8 1.0
OD1 B:ASP561 4.3 61.3 1.0
N B:SER543 4.3 78.6 1.0
NE1 B:TRP566 4.4 55.2 1.0
CB B:ASP541 4.4 77.0 1.0
CG B:ASP561 4.5 51.5 1.0
CG2 B:THR538 4.6 61.1 1.0
N B:THR544 4.8 61.3 1.0
CZ2 B:TRP566 4.9 55.2 1.0
N B:ILE539 5.0 70.2 1.0

Calcium binding site 8 out of 8 in 7xeb

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Calcium binding site 8 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:78.3
occ:1.00
 O B:GLU173 2.7 63.0 1.0
O B:ILE179 2.8 64.3 1.0
O B:ASN176 3.3 71.6 1.0
OG1 B:THR180 3.8 55.0 1.0
C B:GLU173 3.9 61.9 1.0
C B:ILE179 4.0 62.4 1.0
CG B:GLU173 4.2 57.6 1.0
C B:ASN176 4.4 72.4 1.0
CA B:SER177 4.4 72.9 1.0
O B:SER177 4.4 67.6 1.0
CA B:GLU173 4.6 57.1 1.0
C B:SER177 4.6 66.8 1.0
CA B:THR180 4.7 64.8 1.0
N B:THR180 4.7 59.8 1.0
CB B:THR180 4.7 59.2 1.0
N B:ILE179 4.8 68.4 1.0
N B:SER177 4.8 70.5 1.0
N B:PHE174 4.9 63.6 1.0
CA B:ILE179 4.9 62.0 1.0
O B:PHE174 5.0 65.7 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 05:56:57 2024

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