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Zinc in PDB 3shi: Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution

Enzymatic activity of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution

All present enzymatic activity of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution:
3.4.24.7;

Protein crystallography data

The structure of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution, PDB code: 3shi was solved by I.Bertini, V.Calderone, L.Cerofolini, M.Fragai, C.F.G.C.Geraldes, P.Hermann, C.Luchinat, G.Parigi, J.Teixeira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.65 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.694, 54.528, 94.905, 90.00, 120.69, 90.00
R / Rfree (%) 20.9 / 27.8

Other elements in 3shi:

The structure of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution (pdb code 3shi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution, PDB code: 3shi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3shi

Go back to Zinc Binding Sites List in 3shi
Zinc binding site 1 out of 6 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:26.4
occ:1.00
 NE2 A:HIS228 2.1 21.5 1.0
NE2 A:HIS218 2.2 23.9 1.0
NE2 A:HIS222 2.3 26.1 1.0
O A:HOH287 2.4 47.2 1.0
CD2 A:HIS228 3.0 20.6 1.0
CD2 A:HIS218 3.0 24.0 1.0
CE1 A:HIS228 3.1 22.3 1.0
CD2 A:HIS222 3.2 25.3 1.0
CE1 A:HIS218 3.2 20.3 1.0
CE1 A:HIS222 3.3 26.3 1.0
O A:HOH13 4.1 24.9 1.0
CG A:HIS228 4.2 21.4 1.0
ND1 A:HIS228 4.2 20.1 1.0
O A:HOH102 4.2 35.4 1.0
CG A:HIS218 4.2 19.7 1.0
ND1 A:HIS218 4.3 20.2 1.0
CG A:HIS222 4.3 26.7 1.0
ND1 A:HIS222 4.4 30.3 1.0
O A:HOH271 4.4 45.9 1.0
O A:PRO238 4.7 24.6 1.0
CE A:MET236 4.8 20.2 1.0
OE1 A:GLU219 4.8 22.7 1.0
OE2 A:GLU219 4.9 23.1 1.0

Zinc binding site 2 out of 6 in 3shi

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Zinc binding site 2 out of 6 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:25.9
occ:1.00
 OD2 A:ASP170 1.9 25.2 1.0
NE2 A:HIS183 2.0 24.8 1.0
ND1 A:HIS196 2.0 26.3 1.0
NE2 A:HIS168 2.0 25.3 1.0
CE1 A:HIS183 2.8 24.4 1.0
CG A:ASP170 2.8 28.9 1.0
CD2 A:HIS168 2.9 23.7 1.0
CE1 A:HIS196 2.9 27.2 1.0
CD2 A:HIS183 3.1 24.7 1.0
CG A:HIS196 3.1 25.4 1.0
CE1 A:HIS168 3.1 23.4 1.0
OD1 A:ASP170 3.2 24.7 1.0
CB A:HIS196 3.5 24.4 1.0
ND1 A:HIS183 4.0 24.1 1.0
CG A:HIS168 4.1 26.5 1.0
NE2 A:HIS196 4.1 22.0 1.0
O A:SER172 4.1 26.1 1.0
CG A:HIS183 4.1 24.5 1.0
ND1 A:HIS168 4.1 26.1 1.0
CB A:ASP170 4.2 32.9 1.0
CD2 A:HIS196 4.2 24.2 1.0
CE1 A:PHE185 4.4 20.0 1.0
CZ A:PHE185 4.7 21.3 1.0
CE2 A:PHE174 4.7 26.6 1.0
CB A:SER172 4.8 32.9 1.0
O A:HOH9 4.9 27.4 1.0
CG2 A:VAL164 4.9 28.9 1.0
CZ A:PHE174 4.9 26.4 1.0

Zinc binding site 3 out of 6 in 3shi

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Zinc binding site 3 out of 6 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:40.4
occ:1.00
 NE2 G:HIS222 2.1 38.4 1.0
NE2 G:HIS218 2.1 31.8 1.0
NE2 G:HIS228 2.5 59.6 1.0
O G:HOH290 2.6 39.8 1.0
CD2 G:HIS218 3.0 34.7 1.0
CE1 G:HIS222 3.1 35.6 1.0
CD2 G:HIS222 3.1 36.8 1.0
CE1 G:HIS218 3.2 33.0 1.0
CD2 G:HIS228 3.3 54.7 1.0
CE1 G:HIS228 3.5 61.1 1.0
CG G:HIS218 4.2 35.2 1.0
ND1 G:HIS222 4.2 36.2 1.0
O G:HOH307 4.3 41.2 1.0
ND1 G:HIS218 4.3 32.9 1.0
CG G:HIS222 4.3 36.1 1.0
OE1 G:GLU219 4.4 36.4 1.0
CG G:HIS228 4.5 56.7 1.0
O G:HOH295 4.5 31.5 1.0
ND1 G:HIS228 4.5 62.9 1.0
OE2 G:GLU219 4.6 35.5 1.0
CE G:MET236 4.8 31.1 1.0
CD G:GLU219 4.9 31.4 1.0

Zinc binding site 4 out of 6 in 3shi

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Zinc binding site 4 out of 6 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:33.0
occ:1.00
 NE2 G:HIS183 1.9 21.4 1.0
OD2 G:ASP170 2.0 37.5 1.0
ND1 G:HIS196 2.2 30.1 1.0
NE2 G:HIS168 2.3 25.1 1.0
CE1 G:HIS183 2.9 23.1 1.0
CG G:ASP170 2.9 33.0 1.0
CD2 G:HIS183 3.0 23.1 1.0
CD2 G:HIS168 3.0 24.9 1.0
CG G:HIS196 3.1 27.9 1.0
CE1 G:HIS196 3.1 29.0 1.0
OD1 G:ASP170 3.2 32.8 1.0
CB G:HIS196 3.4 24.4 1.0
CE1 G:HIS168 3.4 25.8 1.0
ND1 G:HIS183 4.0 22.6 1.0
CG G:HIS183 4.1 22.2 1.0
O G:SER172 4.2 38.8 1.0
NE2 G:HIS196 4.2 29.4 1.0
CG G:HIS168 4.3 25.5 1.0
CD2 G:HIS196 4.3 29.1 1.0
CB G:ASP170 4.3 32.0 1.0
CE1 G:PHE185 4.4 37.5 1.0
ND1 G:HIS168 4.4 22.8 1.0
CZ G:PHE185 4.4 37.8 1.0
CE2 G:PHE174 4.8 29.5 1.0
CB G:SER172 4.9 35.5 1.0
CA G:HIS196 4.9 25.6 1.0
CZ G:PHE174 5.0 29.7 1.0
O G:HOH44 5.0 28.3 1.0
CG2 G:VAL164 5.0 25.1 1.0

Zinc binding site 5 out of 6 in 3shi

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Zinc binding site 5 out of 6 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn301

b:45.5
occ:1.00
 NE2 M:HIS218 2.0 26.6 1.0
NE2 M:HIS228 2.1 50.7 1.0
NE2 M:HIS222 2.3 42.6 1.0
O M:HOH70 2.4 41.9 1.0
O M:HOH268 2.7 43.4 1.0
CD2 M:HIS228 2.7 54.7 1.0
CD2 M:HIS218 2.9 30.2 1.0
CE1 M:HIS218 3.0 28.7 1.0
CD2 M:HIS222 3.1 35.5 1.0
CE1 M:HIS228 3.3 56.5 1.0
CE1 M:HIS222 3.4 42.0 1.0
CG M:HIS228 4.0 48.8 1.0
ND1 M:HIS218 4.1 26.9 1.0
CG M:HIS218 4.1 27.1 1.0
O M:HOH285 4.1 50.0 1.0
ND1 M:HIS228 4.2 52.1 1.0
CG M:HIS222 4.3 41.1 1.0
O M:HOH264 4.4 38.2 1.0
ND1 M:HIS222 4.4 43.8 1.0
OE2 M:GLU219 4.7 36.6 1.0
OE1 M:GLU219 4.7 48.2 1.0
CA M:PRO238 4.9 49.7 1.0

Zinc binding site 6 out of 6 in 3shi

Go back to Zinc Binding Sites List in 3shi
Zinc binding site 6 out of 6 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn302

b:53.4
occ:1.00
 NE2 M:HIS183 1.8 45.3 1.0
OD2 M:ASP170 2.0 61.3 1.0
ND1 M:HIS196 2.1 38.3 1.0
NE2 M:HIS168 2.5 60.8 1.0
CE1 M:HIS183 2.8 50.5 1.0
CD2 M:HIS183 2.8 49.2 1.0
CG M:ASP170 3.0 63.7 1.0
CE1 M:HIS196 3.0 35.0 1.0
CG M:HIS196 3.1 34.7 1.0
CD2 M:HIS168 3.2 64.8 1.0
CB M:HIS196 3.4 36.4 1.0
OD1 M:ASP170 3.4 64.4 1.0
CE1 M:HIS168 3.6 60.4 1.0
ND1 M:HIS183 3.9 50.6 1.0
CG M:HIS183 3.9 48.5 1.0
O M:SER172 4.0 71.3 1.0
NE2 M:HIS196 4.2 37.8 1.0
CD2 M:HIS196 4.2 34.9 1.0
CB M:ASP170 4.3 69.3 1.0
CE1 M:PHE185 4.3 64.2 1.0
CG M:HIS168 4.5 65.9 1.0
CE2 M:PHE174 4.5 69.6 1.0
ND1 M:HIS168 4.6 63.2 1.0
CZ M:PHE185 4.7 63.8 1.0
CA M:HIS196 4.9 38.7 1.0
CG2 M:VAL164 5.0 48.6 1.0

Reference:

I.Bertini, V.Calderone, L.Cerofolini, M.Fragai, C.F.Geraldes, P.Hermann, C.Luchinat, G.Parigi, J.M.Teixeira. The Catalytic Domain of Mmp-1 Studied Through Tagged Lanthanides. Febs Lett. V. 586 557 2012.
ISSN: ISSN 0014-5793
PubMed: 21945315
DOI: 10.1016/J.FEBSLET.2011.09.020
Page generated: Wed Aug 20 14:02:35 2025

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