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Zinc in PDB 5th6: Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)

Enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)

All present enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9):
3.4.24.35;

Protein crystallography data

The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9), PDB code: 5th6 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) 46.22 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.546, 69.233, 84.093, 90.00, 101.77, 90.00
R / Rfree (%) 20.8 / 23.5

Other elements in 5th6:

The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) (pdb code 5th6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9), PDB code: 5th6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5th6

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Zinc binding site 1 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


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 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:8.9
occ:1.00
NE2 A:HIS411 2.0 8.2 1.0
NE2 A:HIS405 2.0 5.9 1.0
NE2 A:HIS401 2.1 6.0 1.0
SG A:CYS99 2.2 9.2 1.0
CD2 A:HIS411 2.8 10.7 1.0
CB A:CYS99 3.0 11.7 1.0
CD2 A:HIS405 3.0 8.6 1.0
CD2 A:HIS401 3.1 7.1 1.0
CE1 A:HIS405 3.1 9.0 1.0
CE1 A:HIS401 3.1 7.8 1.0
CE1 A:HIS411 3.1 8.3 1.0
CG A:HIS411 4.0 11.6 1.0
CB A:VAL101 4.0 9.5 1.0
ND1 A:HIS411 4.1 10.5 1.0
CG2 A:VAL101 4.1 7.7 1.0
CG A:HIS405 4.1 9.3 1.0
ND1 A:HIS405 4.2 10.6 1.0
ND1 A:HIS401 4.2 8.2 1.0
CG A:HIS401 4.2 8.0 1.0
OE1 A:GLU402 4.4 9.1 1.0
CA A:CYS99 4.4 8.2 1.0
OE2 A:GLU402 4.5 9.4 1.0
CE A:MET419 4.7 9.8 1.0
CD A:GLU402 4.7 7.9 1.0
N A:VAL101 4.8 9.3 1.0
CG1 A:VAL101 4.9 9.8 1.0
C A:CYS99 4.9 9.7 1.0
CA A:PRO421 5.0 8.1 1.0
CA A:VAL101 5.0 12.2 1.0

Zinc binding site 2 out of 8 in 5th6

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Zinc binding site 2 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


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 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:14.4
occ:1.00
OD1 A:ASP177 2.0 15.9 1.0
ND1 A:HIS203 2.0 15.3 1.0
NE2 A:HIS175 2.0 13.5 1.0
NE2 A:HIS190 2.1 12.2 1.0
CD2 A:HIS175 2.9 16.5 1.0
CG A:ASP177 2.9 17.8 1.0
CE1 A:HIS203 2.9 15.9 1.0
CE1 A:HIS190 3.0 11.6 1.0
CG A:HIS203 3.1 11.1 1.0
CE1 A:HIS175 3.1 14.3 1.0
CD2 A:HIS190 3.1 14.7 1.0
OD2 A:ASP177 3.3 16.7 1.0
CB A:HIS203 3.4 13.3 1.0
NE2 A:HIS203 4.1 15.9 1.0
CG A:HIS175 4.1 16.0 1.0
ND1 A:HIS190 4.1 11.7 1.0
CD2 A:HIS203 4.2 13.8 1.0
ND1 A:HIS175 4.2 17.0 1.0
CZ A:PHE192 4.2 14.5 1.0
CG A:HIS190 4.2 11.0 1.0
CB A:ASP177 4.3 19.2 1.0
O A:TYR179 4.3 16.4 1.0
CE2 A:PHE192 4.3 15.2 1.0
CZ A:PHE181 4.4 12.6 1.0
O A:HOH658 4.8 18.1 1.0
CE2 A:PHE181 4.8 12.8 1.0
CE1 A:PHE181 4.9 12.0 1.0
CA A:HIS203 4.9 11.5 1.0

Zinc binding site 3 out of 8 in 5th6

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Zinc binding site 3 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


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 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:77.9
occ:1.00
NE2 B:HIS405 2.0 10.0 1.0
NE2 B:HIS401 2.2 7.3 1.0
NE2 B:HIS411 2.2 10.4 1.0
SG B:CYS99 2.3 8.2 1.0
CD2 B:HIS405 2.9 11.8 1.0
CD2 B:HIS411 2.9 16.0 1.0
CD2 B:HIS401 3.0 9.7 1.0
CE1 B:HIS405 3.0 14.9 1.0
CB B:CYS99 3.0 14.3 1.0
CE1 B:HIS401 3.3 12.7 1.0
CE1 B:HIS411 3.3 19.2 1.0
CB B:VAL101 3.9 11.4 1.0
CG B:HIS405 4.1 12.6 1.0
CG2 B:VAL101 4.1 9.7 1.0
ND1 B:HIS405 4.1 11.7 1.0
CG B:HIS411 4.1 12.8 1.0
CG B:HIS401 4.2 8.3 1.0
ND1 B:HIS411 4.3 12.9 1.0
ND1 B:HIS401 4.3 7.5 1.0
OE1 B:GLU402 4.3 10.2 1.0
OE2 B:GLU402 4.3 7.2 1.0
CA B:CYS99 4.5 11.0 1.0
CE B:MET419 4.6 11.1 1.0
CD B:GLU402 4.6 10.8 1.0
N B:VAL101 4.7 13.7 1.0
CG1 B:VAL101 4.7 16.7 1.0
CA B:VAL101 4.9 16.1 1.0
C B:CYS99 4.9 17.7 1.0

Zinc binding site 4 out of 8 in 5th6

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Zinc binding site 4 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


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 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:17.4
occ:1.00
OD2 B:ASP177 1.9 17.8 1.0
NE2 B:HIS175 2.0 15.1 1.0
NE2 B:HIS190 2.1 18.1 1.0
ND1 B:HIS203 2.2 18.4 1.0
CG B:ASP177 2.8 24.1 1.0
CD2 B:HIS175 2.9 21.9 1.0
CE1 B:HIS190 3.0 17.8 1.0
CD2 B:HIS190 3.1 15.9 1.0
CE1 B:HIS175 3.1 17.1 1.0
OD1 B:ASP177 3.1 22.4 1.0
CG B:HIS203 3.1 15.7 1.0
CE1 B:HIS203 3.2 14.5 1.0
CB B:HIS203 3.4 14.6 1.0
CG B:HIS175 4.1 20.7 1.0
ND1 B:HIS175 4.1 19.2 1.0
ND1 B:HIS190 4.2 17.6 1.0
CG B:HIS190 4.2 13.3 1.0
O B:TYR179 4.2 18.4 1.0
CZ B:PHE192 4.2 18.6 1.0
CB B:ASP177 4.3 19.6 1.0
NE2 B:HIS203 4.3 17.3 1.0
CD2 B:HIS203 4.3 17.6 1.0
CZ B:PHE181 4.3 14.5 1.0
CE2 B:PHE192 4.4 19.9 1.0
CE2 B:PHE181 4.7 16.6 1.0
CE1 B:PHE181 4.8 16.5 1.0
O B:HOH681 4.8 25.4 1.0
CA B:HIS203 4.9 13.1 1.0
O B:HOH683 4.9 21.1 1.0

Zinc binding site 5 out of 8 in 5th6

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Zinc binding site 5 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


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 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:7.0
occ:1.00
NE2 C:HIS411 2.0 9.1 1.0
NE2 C:HIS405 2.0 5.5 1.0
NE2 C:HIS401 2.1 6.4 1.0
SG C:CYS99 2.3 8.3 1.0
CD2 C:HIS411 2.9 7.4 1.0
CD2 C:HIS401 2.9 6.4 1.0
CB C:CYS99 2.9 6.8 1.0
CD2 C:HIS405 3.0 7.4 1.0
CE1 C:HIS411 3.1 7.3 1.0
CE1 C:HIS405 3.1 6.5 1.0
CE1 C:HIS401 3.1 7.0 1.0
CB C:VAL101 4.0 8.4 1.0
CG C:HIS411 4.1 6.8 1.0
CG C:HIS401 4.1 6.8 1.0
ND1 C:HIS411 4.1 8.3 1.0
CG C:HIS405 4.1 6.8 1.0
ND1 C:HIS405 4.2 7.9 1.0
ND1 C:HIS401 4.2 7.1 1.0
CG2 C:VAL101 4.2 8.1 1.0
OE1 C:GLU402 4.3 6.7 1.0
OE2 C:GLU402 4.4 8.3 1.0
CA C:CYS99 4.4 9.1 1.0
CD C:GLU402 4.7 6.0 1.0
CE C:MET419 4.8 7.4 1.0
N C:VAL101 4.8 7.5 1.0
CG1 C:VAL101 4.8 8.8 1.0
C C:CYS99 5.0 10.1 1.0
CA C:VAL101 5.0 9.1 1.0

Zinc binding site 6 out of 8 in 5th6

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Zinc binding site 6 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


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 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:11.4
occ:1.00
OD2 C:ASP177 1.9 13.3 1.0
ND1 C:HIS203 2.0 11.6 1.0
NE2 C:HIS175 2.0 12.1 1.0
NE2 C:HIS190 2.1 10.6 1.0
CG C:ASP177 2.9 15.8 1.0
CE1 C:HIS203 2.9 11.3 1.0
CE1 C:HIS190 3.0 11.2 1.0
CE1 C:HIS175 3.0 14.1 1.0
CD2 C:HIS175 3.0 12.5 1.0
CG C:HIS203 3.0 9.6 1.0
CD2 C:HIS190 3.1 10.3 1.0
OD1 C:ASP177 3.3 11.9 1.0
CB C:HIS203 3.4 7.9 1.0
NE2 C:HIS203 4.1 11.6 1.0
ND1 C:HIS175 4.1 11.0 1.0
ND1 C:HIS190 4.1 10.4 1.0
CZ C:PHE192 4.1 11.2 1.0
CD2 C:HIS203 4.1 12.9 1.0
CG C:HIS175 4.2 12.2 1.0
O C:TYR179 4.2 11.9 1.0
CG C:HIS190 4.2 10.1 1.0
CB C:ASP177 4.2 13.8 1.0
CE2 C:PHE192 4.3 12.0 1.0
CZ C:PHE181 4.3 12.1 1.0
CE2 C:PHE181 4.7 12.1 1.0
O C:HOH654 4.9 15.5 1.0
CE1 C:PHE181 4.9 11.4 1.0
CA C:HIS203 4.9 9.6 1.0
CB C:TYR179 4.9 14.6 1.0

Zinc binding site 7 out of 8 in 5th6

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Zinc binding site 7 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:8.8
occ:1.00
NE2 D:HIS411 2.0 11.5 1.0
NE2 D:HIS405 2.0 7.8 1.0
NE2 D:HIS401 2.1 5.7 1.0
SG D:CYS99 2.3 8.4 1.0
CD2 D:HIS411 2.9 10.2 1.0
CD2 D:HIS405 3.0 7.7 1.0
CB D:CYS99 3.0 7.9 1.0
CD2 D:HIS401 3.0 8.0 1.0
CE1 D:HIS405 3.0 9.5 1.0
CE1 D:HIS411 3.0 10.0 1.0
CE1 D:HIS401 3.1 7.3 1.0
CB D:VAL101 4.0 8.2 1.0
CG D:HIS411 4.0 11.2 1.0
ND1 D:HIS411 4.1 10.5 1.0
ND1 D:HIS405 4.1 8.0 1.0
CG D:HIS405 4.1 9.4 1.0
CG D:HIS401 4.2 7.9 1.0
ND1 D:HIS401 4.2 6.0 1.0
CG2 D:VAL101 4.2 8.4 1.0
OE1 D:GLU402 4.3 9.0 1.0
OE2 D:GLU402 4.4 7.0 1.0
CA D:CYS99 4.5 9.8 1.0
CD D:GLU402 4.7 7.5 1.0
CE D:MET419 4.7 7.2 1.0
N D:VAL101 4.8 9.3 1.0
CG1 D:VAL101 4.8 10.6 1.0
C D:CYS99 4.9 11.4 1.0
CA D:VAL101 5.0 9.2 1.0

Zinc binding site 8 out of 8 in 5th6

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Zinc binding site 8 out of 8 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:13.7
occ:1.00
OD2 D:ASP177 1.9 13.3 1.0
NE2 D:HIS190 2.0 11.2 1.0
ND1 D:HIS203 2.0 12.8 1.0
NE2 D:HIS175 2.1 13.5 1.0
CE1 D:HIS190 2.8 14.1 1.0
CG D:ASP177 2.9 18.6 1.0
CD2 D:HIS175 3.0 16.1 1.0
CE1 D:HIS203 3.0 14.3 1.0
CG D:HIS203 3.1 12.8 1.0
CD2 D:HIS190 3.1 14.1 1.0
OD1 D:ASP177 3.2 16.2 1.0
CE1 D:HIS175 3.2 13.2 1.0
CB D:HIS203 3.4 11.3 1.0
ND1 D:HIS190 4.0 12.2 1.0
CZ D:PHE192 4.1 14.5 1.0
NE2 D:HIS203 4.1 13.1 1.0
CG D:HIS190 4.2 9.2 1.0
CG D:HIS175 4.2 17.0 1.0
CD2 D:HIS203 4.2 13.8 1.0
O D:TYR179 4.2 13.8 1.0
CB D:ASP177 4.2 17.2 1.0
ND1 D:HIS175 4.2 14.5 1.0
CE2 D:PHE192 4.3 15.6 1.0
CZ D:PHE181 4.5 11.5 1.0
CE2 D:PHE181 4.8 13.4 1.0
O D:HOH650 4.9 16.6 1.0
CB D:TYR179 4.9 17.5 1.0
CA D:HIS203 4.9 11.4 1.0
O D:HOH700 5.0 24.9 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: Wed Dec 16 10:55:47 2020

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