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Calcium in PDB 8jt1: Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-Gly-Pro-Hyp

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

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

Protein crystallography data

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-Gly-Pro-Hyp, PDB code: 8jt1 was solved by S.Ueshima, K.Yaskawa, T.Takita, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.44 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 178.017, 74.89, 135.134, 90, 126.02, 90
R / Rfree (%) 17.6 / 21.4

Other elements in 8jt1:

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp (pdb code 8jt1). 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-Gly-Pro-Hyp, PDB code: 8jt1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8jt1

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Calcium binding site 1 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:21.4
occ:1.00
 O A:MET504 2.3 22.0 1.0
O A:GLY500 2.3 22.4 1.0
O A:GLY506 2.3 21.3 1.0
O A:HOH831 2.4 21.3 1.0
OE2 A:GLU461 2.5 23.7 1.0
O A:HOH900 2.5 21.0 1.0
C A:GLY500 3.4 27.7 1.0
CD A:GLU461 3.4 28.8 1.0
C A:GLY506 3.5 24.1 1.0
C A:MET504 3.5 23.8 1.0
OE1 A:GLU461 3.7 23.3 1.0
N A:GLY506 3.8 24.9 1.0
CA A:GLY500 3.9 26.3 1.0
C A:TYR505 4.0 22.4 1.0
O A:HOH811 4.1 18.2 1.0
O A:HOH856 4.2 27.3 1.0
CA A:GLY506 4.3 20.9 1.0
OD2 A:ASP425 4.3 27.3 1.0
O A:TYR505 4.3 23.3 1.0
CB A:MET504 4.4 22.7 1.0
CA A:TYR505 4.4 22.9 1.0
N A:TYR505 4.4 29.4 1.0
CG A:PRO464 4.5 26.7 1.0
CA A:MET504 4.5 23.3 1.0
N A:ARG501 4.6 23.3 1.0
N A:ASP507 4.6 25.4 1.0
O A:HOH902 4.6 20.7 1.0
CA A:ASP507 4.8 27.3 1.0
CG A:GLU461 4.8 20.3 1.0
CG2 A:VAL422 4.8 23.1 1.0
CA A:ARG501 4.9 23.4 1.0
N A:MET504 5.0 22.3 1.0

Calcium binding site 2 out of 8 in 8jt1

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Calcium binding site 2 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:33.0
occ:1.00
 O A:HOH985 2.3 36.4 1.0
OD1 A:ASN436 2.3 32.6 1.0
O A:ASP391 2.4 33.9 1.0
O A:HOH867 2.5 30.6 1.0
OE2 A:GLU477 2.5 27.1 1.0
OE1 A:GLU477 2.5 29.5 1.0
O A:HOH905 2.5 32.9 1.0
CD A:GLU477 2.8 30.4 1.0
CG A:ASN436 3.5 33.0 1.0
C A:ASP391 3.5 28.2 1.0
CG A:GLU477 4.2 24.6 1.0
ND2 A:ASN436 4.2 36.1 1.0
O A:HOH922 4.3 46.9 1.0
CB A:ASP391 4.3 25.9 1.0
N A:MET392 4.4 29.4 1.0
CA A:MET392 4.4 31.2 1.0
OE1 A:GLN396 4.4 31.6 1.0
C2 A:EDO740 4.4 39.3 1.0
O A:ASN436 4.5 28.5 1.0
CA A:ASP391 4.5 35.2 1.0
O2 A:EDO740 4.5 46.6 1.0
CB A:ASN436 4.6 25.4 1.0
CG A:ASP391 4.6 41.0 1.0
OD2 A:ASP391 4.6 37.3 1.0
CA A:ASN436 4.6 30.7 1.0
CB A:GLU477 4.7 24.0 1.0
O A:HOH825 4.7 27.8 1.0
NE2 A:GLN396 4.8 26.2 1.0
O1 A:EDO740 5.0 47.0 1.0
CG A:MET392 5.0 33.8 1.0

Calcium binding site 3 out of 8 in 8jt1

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Calcium binding site 3 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:35.4
occ:1.00
 O A:SER543 2.3 39.0 1.0
O A:HOH911 2.4 31.4 1.0
O A:HOH906 2.4 34.7 1.0
O A:THR538 2.4 36.4 1.0
OG A:SER543 2.4 37.6 1.0
OD1 A:ASP541 2.4 37.3 1.0
OG1 A:THR538 2.5 35.3 1.0
OD2 A:ASP541 2.6 39.5 1.0
CG A:ASP541 2.9 41.4 1.0
C A:THR538 3.3 28.9 1.0
C A:SER543 3.4 38.4 1.0
CA A:THR538 3.5 31.8 1.0
CB A:THR538 3.5 34.7 1.0
CB A:SER543 3.6 33.4 1.0
CA A:SER543 3.8 42.2 1.0
N A:SER543 3.9 43.6 1.0
CB A:ASP541 4.4 42.7 1.0
NE1 A:TRP566 4.4 27.5 1.0
CG2 A:THR538 4.4 30.6 1.0
OD1 A:ASP561 4.5 32.2 1.0
O A:HOH1039 4.5 40.6 1.0
OD2 A:ASP561 4.5 28.2 1.0
N A:THR544 4.5 36.5 1.0
N A:ILE539 4.6 35.6 1.0
CZ2 A:TRP566 4.8 34.6 1.0
CG A:ASP561 4.9 33.3 1.0
N A:THR538 4.9 39.3 1.0

Calcium binding site 4 out of 8 in 8jt1

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Calcium binding site 4 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:30.0
occ:1.00
 O A:ASN176 2.2 46.5 1.0
O A:GLU173 2.3 43.1 1.0
O A:ILE179 2.3 44.5 1.0
O A:HOH928 2.5 41.6 1.0
C A:ASN176 3.2 45.8 1.0
C A:GLU173 3.4 49.1 1.0
C A:ILE179 3.5 38.2 1.0
CA A:SER177 3.7 50.7 1.0
N A:SER177 3.9 49.8 1.0
N A:ILE179 3.9 49.0 1.0
CA A:GLU173 4.0 38.9 1.0
C A:SER177 4.0 47.4 1.0
OG1 A:THR180 4.2 54.2 1.0
CA A:ILE179 4.2 44.3 1.0
O A:SER177 4.2 46.3 1.0
N A:ASN176 4.2 40.2 1.0
CG A:GLU173 4.2 46.0 1.0
CA A:ASN176 4.3 44.9 1.0
O A:PHE174 4.4 37.8 1.0
CB A:ILE179 4.4 41.9 1.0
N A:PHE174 4.5 44.4 1.0
C A:PHE174 4.6 42.2 1.0
N A:THR180 4.6 38.4 1.0
O A:ALA172 4.6 42.9 1.0
N A:ASN178 4.7 47.2 1.0
CB A:GLU173 4.8 47.0 1.0
CA A:PHE174 4.8 45.8 1.0
CA A:THR180 4.8 45.1 1.0

Calcium binding site 5 out of 8 in 8jt1

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Calcium binding site 5 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:23.9
occ:1.00
 O B:GLY506 2.3 23.1 1.0
O B:GLY500 2.3 21.6 1.0
O B:HOH892 2.3 20.4 1.0
O B:MET504 2.3 23.6 1.0
OE2 B:GLU461 2.3 23.6 1.0
O B:HOH876 2.4 21.5 1.0
CD B:GLU461 3.3 26.5 1.0
C B:GLY500 3.3 22.5 1.0
C B:GLY506 3.4 24.6 1.0
C B:MET504 3.5 23.0 1.0
OE1 B:GLU461 3.6 26.4 1.0
N B:GLY506 3.7 22.4 1.0
CA B:GLY500 3.8 19.1 1.0
C B:TYR505 3.9 26.6 1.0
O B:HOH836 4.1 20.6 1.0
O B:HOH823 4.2 24.9 1.0
CA B:GLY506 4.2 24.3 1.0
O B:TYR505 4.3 19.4 1.0
OD2 B:ASP425 4.3 22.7 1.0
CB B:MET504 4.4 24.6 1.0
CA B:TYR505 4.4 23.1 1.0
N B:TYR505 4.4 24.7 1.0
CG B:PRO464 4.4 24.6 1.0
CA B:MET504 4.5 25.9 1.0
N B:ARG501 4.5 18.0 1.0
N B:ASP507 4.5 25.2 1.0
O B:HOH917 4.6 25.0 1.0
CG B:GLU461 4.7 19.8 1.0
CA B:ASP507 4.7 26.3 1.0
CG2 B:VAL422 4.7 18.6 1.0
CA B:ARG501 4.9 21.0 1.0
N B:MET504 5.0 24.3 1.0

Calcium binding site 6 out of 8 in 8jt1

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Calcium binding site 6 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:30.0
occ:1.00
 OD1 B:ASN436 2.1 30.8 1.0
O B:ASP391 2.3 26.6 1.0
O B:HOH869 2.4 31.9 1.0
OE2 B:GLU477 2.5 26.9 1.0
O B:HOH835 2.5 38.9 1.0
OE1 B:GLU477 2.5 28.6 1.0
O B:HOH870 2.5 33.8 1.0
CD B:GLU477 2.8 25.3 1.0
CG B:ASN436 3.4 33.2 1.0
C B:ASP391 3.5 27.4 1.0
ND2 B:ASN436 4.1 34.5 1.0
CB B:ASP391 4.2 29.5 1.0
CG B:GLU477 4.2 23.0 1.0
OD2 B:ASP391 4.3 41.0 1.0
N B:MET392 4.4 29.6 1.0
CA B:MET392 4.4 25.9 1.0
CG B:ASP391 4.4 42.7 1.0
CA B:ASP391 4.4 32.4 1.0
CB B:ASN436 4.4 26.8 1.0
O B:ASN436 4.5 29.5 1.0
OE1 B:GLN396 4.5 30.3 1.0
CA B:ASN436 4.5 27.6 1.0
O B:HOH860 4.6 27.3 1.0
O B:HOH844 4.7 47.1 1.0
CB B:GLU477 4.7 21.5 1.0
NE2 B:GLN396 4.8 24.6 1.0
C1 B:EDO708 4.9 30.0 1.0
CG B:MET392 4.9 30.9 1.0
N B:ASP391 5.0 30.2 1.0
O2 B:EDO708 5.0 47.5 1.0

Calcium binding site 7 out of 8 in 8jt1

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Calcium binding site 7 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:33.9
occ:1.00
 O B:HOH920 2.2 36.2 1.0
O B:THR538 2.3 29.1 1.0
O B:SER543 2.4 37.7 1.0
O B:HOH839 2.4 30.4 1.0
OG1 B:THR538 2.4 38.1 1.0
OD1 B:ASP541 2.5 34.1 1.0
OG B:SER543 2.5 37.3 1.0
OD2 B:ASP541 2.6 37.0 1.0
CG B:ASP541 2.9 35.7 1.0
C B:THR538 3.2 31.1 1.0
C B:SER543 3.4 38.4 1.0
CA B:THR538 3.4 34.8 1.0
CB B:THR538 3.5 36.6 1.0
CB B:SER543 3.7 37.4 1.0
CA B:SER543 3.9 40.1 1.0
N B:SER543 3.9 41.7 1.0
NE1 B:TRP566 4.4 28.5 1.0
OD1 B:ASP561 4.4 34.5 1.0
CB B:ASP541 4.5 38.6 1.0
CG2 B:THR538 4.5 30.4 1.0
N B:ILE539 4.5 31.7 1.0
N B:THR544 4.6 39.0 1.0
O B:HOH1042 4.6 38.0 1.0
OD2 B:ASP561 4.6 31.4 1.0
CZ2 B:TRP566 4.8 31.0 1.0
N B:THR538 4.9 34.1 1.0
CG B:ASP561 4.9 33.3 1.0

Calcium binding site 8 out of 8 in 8jt1

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Calcium binding site 8 out of 8 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp-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-Gly-Pro-Hyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:62.1
occ:1.00
 O B:ILE179 2.3 44.0 1.0
O B:ASN176 2.3 40.8 1.0
O B:GLU173 2.4 46.0 1.0
C B:ASN176 3.3 43.4 1.0
C B:ILE179 3.4 36.9 1.0
C B:GLU173 3.5 44.2 1.0
CA B:SER177 3.7 47.4 1.0
N B:ILE179 3.8 42.9 1.0
N B:SER177 4.0 47.9 1.0
C B:SER177 4.0 49.7 1.0
CA B:ILE179 4.0 41.7 1.0
CA B:GLU173 4.1 36.2 1.0
OG1 B:THR180 4.2 50.3 1.0
O B:SER177 4.3 45.2 1.0
CB B:ILE179 4.4 45.9 1.0
N B:ASN176 4.4 43.0 1.0
N B:THR180 4.4 40.4 1.0
CA B:ASN176 4.4 41.2 1.0
O B:PHE174 4.5 39.3 1.0
CG B:GLU173 4.5 38.7 1.0
N B:ASN178 4.6 49.1 1.0
O B:ALA172 4.6 38.7 1.0
N B:PHE174 4.6 35.2 1.0
C B:PHE174 4.7 37.2 1.0
CA B:THR180 4.7 42.8 1.0
CA B:PHE174 4.9 37.3 1.0
CB B:GLU173 4.9 39.5 1.0
C B:ASN178 5.0 53.5 1.0

Reference:

S.Ueshima, M.Yasumoto, Y.Kitagawa, K.Akazawa, T.Takita, K.Tanaka, S.Hattori, K.Mizutani, B.Mikami, K.Yasukawa. Insights Into the Catalytic Mechanism of Grimontia Hollisae Collagenase Through Structural and Mutational Analyses. Febs Lett. V. 597 2473 2023.
ISSN: ISSN 0014-5793
PubMed: 37698340
DOI: 10.1002/1873-3468.14732
Page generated: Thu Jul 10 05:37:40 2025

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