Atomistry » Zinc » PDB 5th6-5tt3 » 5th9
Atomistry »
  Zinc »
    PDB 5th6-5tt3 »
      5th9 »

Zinc in PDB 5th9: Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)

Enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)

All present enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9):
3.4.24.35;

Protein crystallography data

The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9), PDB code: 5th9 was solved by T.C.Appleby, A.E.Greenstein, H.J.Kwon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.64 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 168.167, 168.167, 234.735, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.7

Other elements in 5th9:

The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) also contains other interesting chemical elements:

Cobalt (Co) 3 atoms
Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) (pdb code 5th9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9), PDB code: 5th9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5th9

Go back to Zinc Binding Sites List in 5th9
Zinc binding site 1 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:15.4
occ:1.00
 NE2 A:HIS411 1.8 18.5 1.0
NE2 A:HIS405 1.8 12.3 1.0
NE2 A:HIS401 1.9 12.2 1.0
SG A:CYS99 2.1 27.8 1.0
CD2 A:HIS411 2.6 18.8 1.0
CE1 A:HIS401 2.8 18.7 1.0
CD2 A:HIS405 2.8 9.4 1.0
CE1 A:HIS405 2.9 10.4 1.0
CB A:CYS99 2.9 21.3 1.0
CD2 A:HIS401 2.9 14.2 1.0
CE1 A:HIS411 3.0 17.3 1.0
CG A:HIS411 3.8 20.1 1.0
ND1 A:HIS401 3.9 20.0 1.0
ND1 A:HIS405 4.0 11.2 1.0
ND1 A:HIS411 4.0 15.9 1.0
CG A:HIS405 4.0 9.2 1.0
CG A:HIS401 4.0 14.8 1.0
CB A:VAL101 4.3 12.3 1.0
CA A:CYS99 4.4 13.4 1.0
OE1 A:GLU402 4.4 13.8 1.0
CG2 A:VAL101 4.6 11.1 1.0
CA A:PRO421 4.8 23.5 1.0
CE A:MET419 4.9 13.3 1.0
C A:CYS99 4.9 15.1 1.0
N A:VAL101 4.9 17.6 1.0
OE2 A:GLU402 4.9 5.7 1.0
CD A:GLU402 5.0 8.7 1.0

Zinc binding site 2 out of 6 in 5th9

Go back to Zinc Binding Sites List in 5th9
Zinc binding site 2 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:5.2
occ:1.00
 OD1 A:ASP177 1.5 13.2 1.0
NE2 A:HIS175 2.0 7.5 1.0
NE2 A:HIS190 2.1 5.2 1.0
ND1 A:HIS203 2.1 7.0 1.0
CG A:ASP177 2.6 9.3 1.0
CD2 A:HIS175 3.0 7.3 1.0
CE1 A:HIS175 3.0 20.9 1.0
CE1 A:HIS203 3.0 12.5 1.0
CE1 A:HIS190 3.0 9.4 1.0
CD2 A:HIS190 3.1 6.2 1.0
CG A:HIS203 3.1 5.5 1.0
OD2 A:ASP177 3.3 17.8 1.0
CB A:HIS203 3.4 5.0 1.0
CB A:ASP177 3.8 10.3 1.0
ND1 A:HIS175 4.1 14.0 1.0
CG A:HIS175 4.1 8.1 1.0
ND1 A:HIS190 4.1 7.3 1.0
O A:TYR179 4.1 13.0 1.0
NE2 A:HIS203 4.2 9.6 1.0
CD2 A:HIS203 4.2 4.6 1.0
CG A:HIS190 4.2 11.1 1.0
CZ A:PHE192 4.3 5.6 1.0
CE2 A:PHE192 4.4 7.4 1.0
CZ A:PHE181 4.5 5.9 1.0
CB A:TYR179 4.8 9.2 1.0
CE2 A:PHE181 4.9 5.8 1.0
CA A:HIS203 4.9 4.4 1.0

Zinc binding site 3 out of 6 in 5th9

Go back to Zinc Binding Sites List in 5th9
Zinc binding site 3 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:13.0
occ:1.00
 NE2 B:HIS405 1.9 13.9 1.0
NE2 B:HIS411 1.9 11.3 1.0
NE2 B:HIS401 2.0 14.7 1.0
SG B:CYS99 2.1 51.0 1.0
CB B:CYS99 2.6 22.9 1.0
CD2 B:HIS411 2.8 20.3 1.0
CD2 B:HIS401 2.9 21.0 1.0
CD2 B:HIS405 2.9 9.3 1.0
CE1 B:HIS405 2.9 14.6 1.0
CE1 B:HIS401 3.0 16.3 1.0
CE1 B:HIS411 3.0 13.1 1.0
CG B:HIS411 4.0 17.4 1.0
ND1 B:HIS405 4.0 11.1 1.0
ND1 B:HIS401 4.1 12.6 1.0
ND1 B:HIS411 4.1 21.0 1.0
CG B:HIS401 4.1 15.9 1.0
CG B:HIS405 4.1 12.3 1.0
CA B:CYS99 4.1 17.9 1.0
CB B:VAL101 4.3 7.4 1.0
OE2 B:GLU402 4.4 17.5 1.0
CG2 B:VAL101 4.5 10.0 1.0
CE B:MET419 4.7 21.9 1.0
C B:CYS99 4.8 14.4 1.0
N B:VAL101 4.8 10.1 1.0
OE1 B:GLU402 4.8 14.9 1.0
CD B:GLU402 4.9 11.7 1.0
N B:CYS99 4.9 17.4 1.0
N B:GLY100 5.0 15.1 1.0

Zinc binding site 4 out of 6 in 5th9

Go back to Zinc Binding Sites List in 5th9
Zinc binding site 4 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:2.8
occ:1.00
 OD1 B:ASP177 1.7 6.6 1.0
NE2 B:HIS175 1.9 6.8 1.0
ND1 B:HIS203 2.0 5.8 1.0
NE2 B:HIS190 2.0 7.3 1.0
CG B:ASP177 2.7 8.8 1.0
CE1 B:HIS190 2.9 6.2 1.0
CE1 B:HIS175 2.9 15.1 1.0
CE1 B:HIS203 2.9 4.2 1.0
CD2 B:HIS175 2.9 7.9 1.0
CG B:HIS203 3.1 5.1 1.0
CD2 B:HIS190 3.1 8.8 1.0
OD2 B:ASP177 3.1 24.3 1.0
CB B:HIS203 3.4 5.3 1.0
ND1 B:HIS175 4.0 14.0 1.0
CG B:HIS175 4.1 10.4 1.0
ND1 B:HIS190 4.1 5.8 1.0
CB B:ASP177 4.1 10.5 1.0
NE2 B:HIS203 4.1 3.8 1.0
CD2 B:HIS203 4.1 4.3 1.0
O B:TYR179 4.2 10.9 1.0
CG B:HIS190 4.2 11.3 1.0
CZ B:PHE192 4.3 7.5 1.0
CE1 B:PHE192 4.5 7.7 1.0
CZ B:PHE181 4.5 9.8 1.0
CB B:TYR179 4.9 11.2 1.0
CE2 B:PHE181 4.9 13.5 1.0
CA B:HIS203 4.9 6.5 1.0

Zinc binding site 5 out of 6 in 5th9

Go back to Zinc Binding Sites List in 5th9
Zinc binding site 5 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:81.4
occ:1.00
 NE2 C:HIS405 2.0 73.0 1.0
NE2 C:HIS401 2.4 0.1 1.0
SG C:CYS99 2.4 86.0 1.0
NE2 C:HIS411 2.8 93.8 1.0
CE1 C:HIS401 2.9 0.1 1.0
CD2 C:HIS405 2.9 72.6 1.0
CB C:CYS99 3.1 91.9 1.0
CE1 C:HIS405 3.1 76.6 1.0
CE1 C:HIS411 3.4 94.7 1.0
CD2 C:HIS401 3.5 91.5 1.0
CD2 C:HIS411 3.8 91.3 1.0
ND1 C:HIS401 4.0 98.2 1.0
CG C:HIS405 4.1 72.2 1.0
ND1 C:HIS405 4.2 73.4 1.0
CB C:VAL101 4.2 88.8 1.0
CG C:HIS401 4.3 84.6 1.0
CG2 C:VAL101 4.4 78.1 1.0
ND1 C:HIS411 4.5 98.4 1.0
O C:VAL101 4.5 0.1 1.0
CA C:CYS99 4.5 89.5 1.0
CG C:HIS411 4.7 93.7 1.0
OE2 C:GLU402 4.7 69.7 1.0
N C:VAL101 4.7 92.0 1.0
OE1 C:GLU402 4.8 66.0 1.0
CA C:VAL101 4.9 97.4 1.0
C C:CYS99 5.0 96.7 1.0

Zinc binding site 6 out of 6 in 5th9

Go back to Zinc Binding Sites List in 5th9
Zinc binding site 6 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:78.4
occ:1.00
 NE2 C:HIS175 2.1 93.8 1.0
CD2 C:HIS203 2.6 77.2 1.0
OD1 C:ASP177 2.8 99.1 1.0
CD2 C:HIS175 2.9 95.9 1.0
NE2 C:HIS190 2.9 89.9 1.0
OD2 C:ASP177 3.0 0.1 1.0
CE1 C:HIS190 3.2 87.1 1.0
CG C:HIS203 3.2 79.8 1.0
CE1 C:HIS175 3.2 94.8 1.0
CG C:ASP177 3.3 0.4 1.0
CB C:HIS203 3.4 81.9 1.0
NE2 C:HIS203 3.7 74.3 1.0
CD2 C:HIS190 4.0 90.3 1.0
CG C:HIS175 4.1 97.0 1.0
O C:TYR179 4.1 0.9 1.0
CZ C:PHE192 4.1 78.1 1.0
ND1 C:HIS175 4.2 95.8 1.0
ND1 C:HIS190 4.3 85.8 1.0
ND1 C:HIS203 4.3 80.9 1.0
CE1 C:HIS203 4.5 74.1 1.0
CE2 C:PHE192 4.6 78.0 1.0
CZ C:PHE181 4.7 94.1 1.0
CG C:HIS190 4.8 83.9 1.0
CB C:ASP177 4.8 1.0 1.0
CA C:HIS203 4.9 77.9 1.0

Reference:

T.C.Appleby, A.E.Greenstein, M.Hung, A.Liclican, M.Velasquez, A.G.Villasenor, R.Wang, M.H.Wong, X.Liu, G.A.Papalia, B.E.Schultz, R.Sakowicz, V.Smith, H.J.Kwon. Biochemical Characterization and Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9. J. Biol. Chem. V. 292 6810 2017.
ISSN: ESSN 1083-351X
PubMed: 28235803
DOI: 10.1074/JBC.M116.760579
Page generated: Mon Oct 28 08:32:32 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy