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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

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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

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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

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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

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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

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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

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