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Zinc in PDB 1su3: X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action

Enzymatic activity of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action

All present enzymatic activity of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action:
3.4.24.7;

Protein crystallography data

The structure of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action, PDB code: 1su3 was solved by D.Jozic, G.Bourenkov, N.H.Lim, H.Nagase, W.Bode, K.Maskos, Structural Proteomics In Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.746, 142.746, 295.308, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25.2

Other elements in 1su3:

The structure of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action also contains other interesting chemical elements:

Calcium (Ca) 8 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action (pdb code 1su3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action, PDB code: 1su3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1su3

Go back to Zinc Binding Sites List in 1su3
Zinc binding site 1 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn913

b:34.8
occ:1.00
NE2 A:HIS222 2.0 31.5 1.0
NE2 A:HIS228 2.0 33.8 1.0
NE2 A:HIS218 2.0 31.2 1.0
SG A:CYS92 2.2 27.4 1.0
CD2 A:HIS228 2.9 31.4 1.0
CE1 A:HIS222 2.9 33.8 1.0
CB A:CYS92 3.0 29.1 1.0
CD2 A:HIS222 3.0 34.2 1.0
CD2 A:HIS218 3.0 30.2 1.0
CE1 A:HIS218 3.0 31.5 1.0
CE1 A:HIS228 3.1 35.5 1.0
CB A:VAL94 4.0 29.8 1.0
ND1 A:HIS222 4.1 32.5 1.0
CG A:HIS228 4.1 33.2 1.0
CG A:HIS222 4.1 33.7 1.0
ND1 A:HIS228 4.1 32.4 1.0
ND1 A:HIS218 4.1 27.3 1.0
CG A:HIS218 4.1 28.8 1.0
CG2 A:VAL94 4.3 29.6 1.0
CA A:CYS92 4.4 28.7 1.0
N A:VAL94 4.7 29.6 1.0
CE A:MET236 4.7 32.3 1.0
CG1 A:VAL94 4.9 29.9 1.0
CA A:VAL94 4.9 30.1 1.0
O A:VAL94 4.9 30.5 1.0
C A:CYS92 4.9 29.1 1.0

Zinc binding site 2 out of 4 in 1su3

Go back to Zinc Binding Sites List in 1su3
Zinc binding site 2 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn915

b:42.3
occ:1.00
ND1 A:HIS196 1.8 31.6 1.0
OD2 A:ASP170 2.0 43.6 1.0
NE2 A:HIS183 2.1 36.3 1.0
NE2 A:HIS168 2.1 39.7 1.0
CE1 A:HIS196 2.7 35.0 1.0
CG A:HIS196 2.9 35.1 1.0
CD2 A:HIS168 2.9 39.8 1.0
CG A:ASP170 2.9 42.8 1.0
CE1 A:HIS183 3.0 36.0 1.0
CD2 A:HIS183 3.1 32.8 1.0
OD1 A:ASP170 3.1 39.9 1.0
CE1 A:HIS168 3.2 38.8 1.0
CB A:HIS196 3.4 33.9 1.0
NE2 A:HIS196 3.8 34.4 1.0
CD2 A:HIS196 4.0 36.2 1.0
O A:SER172 4.0 44.3 1.0
CG A:HIS168 4.1 41.5 1.0
ND1 A:HIS183 4.1 35.6 1.0
ND1 A:HIS168 4.2 41.1 1.0
CG A:HIS183 4.2 34.1 1.0
CE1 A:PHE185 4.3 41.1 1.0
CB A:ASP170 4.3 44.9 1.0
CZ A:PHE185 4.5 41.4 1.0
CE2 A:PHE174 4.7 35.6 1.0
CB A:SER172 4.8 45.8 1.0
CZ A:PHE174 4.8 36.8 1.0
O A:HOH978 4.9 49.4 1.0
CA A:HIS196 4.9 34.1 1.0
CG2 A:VAL164 4.9 36.7 1.0

Zinc binding site 3 out of 4 in 1su3

Go back to Zinc Binding Sites List in 1su3
Zinc binding site 3 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn913

b:35.6
occ:1.00
NE2 B:HIS228 1.9 35.0 1.0
NE2 B:HIS218 2.0 33.9 1.0
NE2 B:HIS222 2.0 34.9 1.0
SG B:CYS92 2.3 40.0 1.0
CE1 B:HIS228 2.9 34.1 1.0
CD2 B:HIS228 2.9 32.7 1.0
CB B:CYS92 2.9 39.8 1.0
CD2 B:HIS222 2.9 37.1 1.0
CE1 B:HIS218 3.0 35.6 1.0
CD2 B:HIS218 3.0 33.5 1.0
CE1 B:HIS222 3.1 37.0 1.0
CB B:VAL94 3.9 39.5 1.0
ND1 B:HIS228 4.0 32.5 1.0
CG B:HIS228 4.0 33.8 1.0
ND1 B:HIS218 4.1 35.1 1.0
CG B:HIS222 4.1 35.6 1.0
CG B:HIS218 4.1 33.9 1.0
ND1 B:HIS222 4.1 37.8 1.0
CG2 B:VAL94 4.2 41.0 1.0
CA B:CYS92 4.4 40.0 1.0
CE B:MET236 4.7 35.2 1.0
CG1 B:VAL94 4.8 38.7 1.0
N B:VAL94 4.8 38.7 1.0
C B:CYS92 4.8 39.8 1.0
CA B:VAL94 4.9 39.4 1.0

Zinc binding site 4 out of 4 in 1su3

Go back to Zinc Binding Sites List in 1su3
Zinc binding site 4 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn915

b:45.7
occ:1.00
OD2 B:ASP170 1.7 43.2 1.0
ND1 B:HIS196 1.9 36.3 1.0
NE2 B:HIS183 2.1 41.5 1.0
NE2 B:HIS168 2.2 41.2 1.0
CG B:ASP170 2.8 46.0 1.0
CE1 B:HIS196 2.8 39.9 1.0
CD2 B:HIS168 2.9 41.8 1.0
CE1 B:HIS183 3.0 41.8 1.0
CG B:HIS196 3.0 37.6 1.0
CD2 B:HIS183 3.1 39.9 1.0
OD1 B:ASP170 3.2 41.0 1.0
CE1 B:HIS168 3.4 42.6 1.0
CB B:HIS196 3.4 36.6 1.0
NE2 B:HIS196 3.9 40.4 1.0
O B:SER172 4.0 46.6 1.0
CD2 B:HIS196 4.1 39.6 1.0
CB B:ASP170 4.1 47.4 1.0
ND1 B:HIS183 4.1 41.6 1.0
CG B:HIS168 4.2 43.6 1.0
CG B:HIS183 4.2 39.6 1.0
CE1 B:PHE185 4.3 42.0 1.0
ND1 B:HIS168 4.3 41.6 1.0
CZ B:PHE185 4.5 41.9 1.0
CE2 B:PHE174 4.7 39.6 1.0
CB B:SER172 4.7 47.6 1.0
CZ B:PHE174 4.8 39.5 1.0
CG2 B:VAL164 4.9 40.3 1.0
O B:HOH946 4.9 50.2 1.0
CA B:HIS196 4.9 36.5 1.0
C B:SER172 5.0 46.9 1.0

Reference:

D.Jozic, G.Bourenkov, N.H.Lim, R.Visse, H.Nagase, W.Bode, K.Maskos. X-Ray Structure of Human Prommp-1: New Insights Into Procollagenase Activation and Collagen Binding. J.Biol.Chem. V. 280 9578 2005.
ISSN: ISSN 0021-9258
PubMed: 15611040
DOI: 10.1074/JBC.M411084200
Page generated: Mon Jan 25 16:13:31 2021

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