Calcium in PDB 6qig: Metalloproteinase

Enzymatic activity of Metalloproteinase

All present enzymatic activity of Metalloproteinase:
3.4.24.87;

Protein crystallography data

The structure of Metalloproteinase, PDB code: 6qig was solved by H.J.Kim, J.Emsley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.20 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.532, 87.532, 407.342, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 24.7

Other elements in 6qig:

The structure of Metalloproteinase also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Metalloproteinase (pdb code 6qig). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Metalloproteinase, PDB code: 6qig:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6qig

Go back to Calcium Binding Sites List in 6qig
Calcium binding site 1 out of 3 in the Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca717

b:51.7
occ:1.00
O A:LEU183 2.3 50.2 1.0
OD1 A:ASP182 2.3 58.8 1.0
OE1 A:GLU212 2.3 59.8 1.0
O A:ARG190 2.3 49.2 1.0
O A:HOH805 2.3 35.4 1.0
O A:VAL192 2.4 51.4 1.0
CD A:GLU212 3.2 62.1 1.0
N A:LEU183 3.2 51.8 1.0
OE2 A:GLU212 3.3 60.6 1.0
C A:LEU183 3.4 55.0 1.0
CG A:ASP182 3.5 60.4 1.0
C A:ARG190 3.5 54.0 1.0
C A:ASP182 3.5 52.9 1.0
C A:VAL192 3.6 50.4 1.0
CA A:LEU183 3.7 52.7 1.0
CA A:ASP182 3.8 54.4 1.0
CB A:LEU183 4.0 55.6 1.0
CA A:ARG190 4.2 58.3 1.0
CB A:ASP182 4.2 55.2 1.0
N A:VAL192 4.3 54.0 1.0
O A:ASP182 4.3 45.4 1.0
OD2 A:ASP182 4.4 57.2 1.0
C A:GLN191 4.4 52.2 1.0
CG1 A:VAL192 4.5 53.5 1.0
N A:GLU184 4.5 53.4 1.0
N A:GLN191 4.6 53.5 1.0
CA A:VAL192 4.6 53.4 1.0
CB A:ARG190 4.6 56.5 1.0
N A:ARG193 4.6 52.5 1.0
CG A:GLU212 4.6 64.8 1.0
O A:GLN191 4.7 58.1 1.0
CA A:ARG193 4.8 49.3 1.0
CA A:GLN191 4.9 56.2 1.0
CA A:GLU184 5.0 50.8 1.0

Calcium binding site 2 out of 3 in 6qig

Go back to Calcium Binding Sites List in 6qig
Calcium binding site 2 out of 3 in the Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca718

b:73.6
occ:1.00
OE1 A:GLU83 2.3 79.6 1.0
O A:CYS281 2.3 79.6 1.0
OD2 A:ASP173 2.3 75.4 1.0
OD2 A:ASP166 2.3 69.8 1.0
OD1 A:ASP173 2.8 73.6 1.0
CD A:GLU83 2.8 83.3 1.0
OE2 A:GLU83 2.8 80.1 1.0
CG A:ASP173 2.9 79.1 1.0
OD1 A:ASP166 2.9 81.2 1.0
OD2 A:ASP284 2.9 89.0 1.0
CG A:ASP166 3.0 75.1 1.0
OD1 A:ASP284 3.4 86.2 1.0
C A:CYS281 3.4 70.3 1.0
CG A:ASP284 3.5 89.3 1.0
CA A:CA719 3.7 79.9 1.0
CG A:GLU83 4.2 82.3 1.0
CA A:CYS281 4.2 80.0 1.0
N A:VAL282 4.3 66.7 1.0
CB A:ASP173 4.4 76.3 1.0
O A:ASP284 4.4 84.1 1.0
CA A:VAL282 4.5 80.2 1.0
CB A:ASP166 4.5 71.1 1.0
O A:HIS81 4.5 67.3 1.0
CB A:CYS281 4.6 89.7 1.0
CB A:GLU83 4.7 76.3 1.0
CB A:ASP284 4.9 84.9 1.0

Calcium binding site 3 out of 3 in 6qig

Go back to Calcium Binding Sites List in 6qig
Calcium binding site 3 out of 3 in the Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca719

b:79.9
occ:1.00
OE2 A:GLU83 2.3 80.1 1.0
O A:ASP166 2.3 0.2 1.0
OD1 A:ASP166 2.3 81.2 1.0
OD2 A:ASP284 3.2 89.0 1.0
CG A:ASP166 3.3 75.1 1.0
CD A:GLU83 3.4 83.3 1.0
C A:ASP166 3.5 97.5 1.0
CA A:CA718 3.7 73.6 1.0
OE1 A:GLU83 4.0 79.6 1.0
OD2 A:ASP166 4.0 69.8 1.0
CG A:ARG287 4.0 0.6 1.0
CA A:ASP166 4.2 82.1 1.0
CB A:ASP166 4.2 71.1 1.0
O A:PRO285 4.3 61.1 1.0
CG A:ASP284 4.4 89.3 1.0
CG A:GLU83 4.6 82.3 1.0
CD A:ARG287 4.6 0.5 1.0
N A:THR167 4.6 0.0 1.0
N A:ARG287 4.7 75.0 1.0
O A:ASP168 4.7 96.1 1.0
CA A:PRO286 4.8 65.3 1.0
CA A:THR167 5.0 0.4 1.0

Reference:

A.Petri, H.J.Kim, Y.Xu, R.De Groot, C.Li, A.Vandenbulcke, K.Vanhoorelbeke, J.Emsley, J.T.B.Crawley. Crystal Structure and Substrate-Induced Activation of ADAMTS13. Nat Commun V. 10 3781 2019.
ISSN: ESSN 2041-1723
PubMed: 31439947
DOI: 10.1038/S41467-019-11474-5
Page generated: Sat Dec 12 07:27:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy