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Zinc in PDB 3ljz: Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound

Protein crystallography data

The structure of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound, PDB code: 3ljz was solved by H.-S.Shieh, J.R.Kiefer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.604, 94.927, 120.406, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.8

Other elements in 3ljz:

The structure of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound (pdb code 3ljz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound, PDB code: 3ljz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3ljz

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Zinc binding site 1 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn998

b:14.1
occ:1.00
 OD2 A:ASP174 1.9 14.9 1.0
ND1 A:HIS200 2.0 15.2 1.0
NE2 A:HIS187 2.0 22.7 1.0
NE2 A:HIS172 2.1 14.3 1.0
CE1 A:HIS187 2.4 23.0 1.0
CG A:ASP174 2.8 14.6 1.0
CD2 A:HIS172 2.9 11.9 1.0
CE1 A:HIS200 3.0 16.3 1.0
CG A:HIS200 3.0 12.9 1.0
OD1 A:ASP174 3.1 13.7 1.0
CE1 A:HIS172 3.2 14.7 1.0
CD2 A:HIS187 3.3 22.0 1.0
CB A:HIS200 3.4 11.5 1.0
ND1 A:HIS187 3.7 23.8 1.0
CG A:HIS172 4.0 12.5 1.0
NE2 A:HIS200 4.1 13.0 1.0
CD2 A:HIS200 4.1 13.6 1.0
CG A:HIS187 4.1 18.9 1.0
ND1 A:HIS172 4.2 14.1 1.0
O A:TYR176 4.2 15.1 1.0
CB A:ASP174 4.2 15.7 1.0
CE1 A:PHE189 4.6 22.9 1.0
CB A:TYR176 4.7 18.9 1.0
O A:HOH24 4.8 7.9 1.0
CZ A:PHE178 4.8 18.3 1.0
CE2 A:PHE178 4.8 17.7 1.0
CA A:HIS200 4.9 11.5 1.0
CZ A:PHE189 4.9 23.7 1.0
C A:TYR176 5.0 17.1 1.0

Zinc binding site 2 out of 8 in 3ljz

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Zinc binding site 2 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn999

b:20.6
occ:1.00
 NE2 A:HIS222 2.0 12.8 1.0
NE2 A:HIS232 2.0 20.6 1.0
NE2 A:HIS226 2.1 16.5 1.0
O23 A:LA3801 2.2 28.5 1.0
O21 A:LA3801 2.6 31.1 1.0
CD2 A:HIS232 2.9 21.3 1.0
CD2 A:HIS222 3.0 14.6 1.0
CE1 A:HIS222 3.0 16.0 1.0
CD2 A:HIS226 3.0 15.9 1.0
CE1 A:HIS226 3.1 20.1 1.0
CE1 A:HIS232 3.1 21.7 1.0
C20 A:LA3801 3.2 30.4 1.0
N22 A:LA3801 3.2 31.3 1.0
CG A:HIS232 4.1 23.3 1.0
ND1 A:HIS222 4.1 15.1 1.0
CG A:HIS222 4.1 14.3 1.0
O A:HOH291 4.1 13.6 1.0
ND1 A:HIS232 4.1 22.3 1.0
ND1 A:HIS226 4.2 17.4 1.0
CG A:HIS226 4.2 16.0 1.0
OE2 A:GLU223 4.4 22.4 1.0
C19 A:LA3801 4.5 29.5 1.0
OE1 A:GLU223 4.5 19.9 1.0
C8 A:LA3801 4.7 24.4 1.0
O A:HOH292 4.7 22.9 1.0
C4 A:LA3801 4.7 21.9 1.0
C17 A:LA3801 4.7 28.7 1.0
CE A:MET240 4.8 19.2 1.0
CD A:GLU223 4.8 18.3 1.0
C5 A:LA3801 4.9 22.7 1.0

Zinc binding site 3 out of 8 in 3ljz

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Zinc binding site 3 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn998

b:12.2
occ:1.00
 ND1 B:HIS200 1.9 12.1 1.0
OD2 B:ASP174 2.0 9.7 1.0
NE2 B:HIS172 2.0 10.2 1.0
CE1 B:HIS187 2.1 15.7 1.0
NE2 B:HIS187 2.3 17.5 1.0
CE1 B:HIS200 2.9 13.9 1.0
CD2 B:HIS172 2.9 11.2 1.0
CG B:ASP174 2.9 11.3 1.0
CG B:HIS200 3.0 10.3 1.0
CE1 B:HIS172 3.1 12.6 1.0
OD1 B:ASP174 3.1 12.0 1.0
CB B:HIS200 3.4 10.5 1.0
ND1 B:HIS187 3.4 17.3 1.0
CD2 B:HIS187 3.7 14.3 1.0
NE2 B:HIS200 4.0 11.6 1.0
CG B:HIS172 4.0 11.9 1.0
CD2 B:HIS200 4.1 10.6 1.0
ND1 B:HIS172 4.1 12.3 1.0
O B:TYR176 4.1 13.9 1.0
CG B:HIS187 4.2 13.5 1.0
CB B:ASP174 4.3 13.6 1.0
CB B:TYR176 4.6 16.1 1.0
CE1 B:PHE189 4.8 20.4 1.0
CZ B:PHE178 4.9 12.6 1.0
CA B:HIS200 4.9 10.0 1.0
C B:TYR176 4.9 15.2 1.0
CE2 B:PHE178 4.9 13.0 1.0
CZ B:PHE189 4.9 20.9 1.0
O B:HOH12 5.0 5.9 1.0

Zinc binding site 4 out of 8 in 3ljz

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Zinc binding site 4 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn999

b:14.6
occ:1.00
 NE2 B:HIS232 2.0 13.0 1.0
NE2 B:HIS222 2.0 8.8 1.0
NE2 B:HIS226 2.0 12.2 1.0
O23 B:LA3802 2.1 24.8 1.0
O21 B:LA3802 2.3 26.8 1.0
C20 B:LA3802 2.9 25.0 1.0
CD2 B:HIS232 2.9 14.7 1.0
N22 B:LA3802 3.0 27.2 1.0
CD2 B:HIS222 3.0 10.0 1.0
CE1 B:HIS226 3.0 13.7 1.0
CE1 B:HIS222 3.0 12.2 1.0
CE1 B:HIS232 3.0 15.1 1.0
CD2 B:HIS226 3.1 11.6 1.0
CG B:HIS232 4.1 16.8 1.0
O2S B:EPE3 4.1 63.5 1.0
ND1 B:HIS232 4.1 15.2 1.0
ND1 B:HIS226 4.1 14.0 1.0
ND1 B:HIS222 4.1 10.9 1.0
CG B:HIS222 4.1 10.0 1.0
CG B:HIS226 4.2 11.8 1.0
O B:HOH4 4.3 14.2 1.0
C19 B:LA3802 4.3 23.2 1.0
OE2 B:GLU223 4.4 19.9 1.0
OE1 B:GLU223 4.4 18.6 1.0
C8 B:LA3802 4.5 19.0 1.0
C17 B:LA3802 4.6 21.0 1.0
C4 B:LA3802 4.7 17.2 1.0
CD B:GLU223 4.7 16.8 1.0
C5 B:LA3802 4.9 18.3 1.0
CE B:MET240 4.9 15.0 1.0

Zinc binding site 5 out of 8 in 3ljz

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Zinc binding site 5 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn998

b:15.5
occ:1.00
 OD2 C:ASP174 1.9 14.2 1.0
ND1 C:HIS200 2.0 16.2 1.0
NE2 C:HIS187 2.0 18.3 1.0
NE2 C:HIS172 2.1 16.6 1.0
CG C:ASP174 2.8 15.7 1.0
CD2 C:HIS172 2.9 14.9 1.0
CE1 C:HIS200 3.0 16.6 1.0
CE1 C:HIS187 3.0 19.5 1.0
CG C:HIS200 3.0 14.0 1.0
CD2 C:HIS187 3.1 18.1 1.0
CE1 C:HIS172 3.1 17.3 1.0
OD1 C:ASP174 3.1 16.4 1.0
CB C:HIS200 3.4 15.0 1.0
NE2 C:HIS200 4.1 14.3 1.0
ND1 C:HIS187 4.1 19.7 1.0
CG C:HIS172 4.1 13.6 1.0
CD2 C:HIS200 4.1 15.2 1.0
ND1 C:HIS172 4.1 15.4 1.0
CG C:HIS187 4.2 18.4 1.0
CB C:ASP174 4.2 15.8 1.0
O C:TYR176 4.2 19.2 1.0
CZ C:PHE178 4.5 17.2 1.0
CE1 C:PHE189 4.6 24.7 1.0
CE2 C:PHE178 4.7 16.6 1.0
CZ C:PHE189 4.7 26.5 1.0
O C:HOH8 4.8 10.1 1.0
CA C:HIS200 4.9 14.1 1.0
O C:HOH290 4.9 18.8 1.0
CB C:TYR176 4.9 21.9 1.0

Zinc binding site 6 out of 8 in 3ljz

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Zinc binding site 6 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn999

b:23.4
occ:1.00
 NE2 C:HIS226 2.0 18.2 1.0
NE2 C:HIS222 2.1 19.3 1.0
NE2 C:HIS232 2.1 27.1 1.0
O21 C:LA3803 2.2 30.8 1.0
O23 C:LA3803 2.3 30.8 1.0
CD2 C:HIS222 2.9 18.2 1.0
CD2 C:HIS232 3.0 27.4 1.0
CD2 C:HIS226 3.0 19.1 1.0
C20 C:LA3803 3.0 30.6 1.0
CE1 C:HIS226 3.0 22.2 1.0
CE1 C:HIS232 3.1 28.4 1.0
CE1 C:HIS222 3.1 24.0 1.0
N22 C:LA3803 3.2 32.4 1.0
ND1 C:HIS226 4.1 21.6 1.0
CG C:HIS226 4.1 19.1 1.0
CG C:HIS222 4.1 18.9 1.0
CG C:HIS232 4.1 30.6 1.0
ND1 C:HIS232 4.2 30.2 1.0
ND1 C:HIS222 4.2 22.0 1.0
O C:HOH10 4.2 8.7 1.0
OE2 C:GLU223 4.3 25.5 1.0
C19 C:LA3803 4.4 27.1 1.0
OE1 C:GLU223 4.5 24.5 1.0
C4 C:LA3803 4.6 26.5 1.0
C8 C:LA3803 4.7 24.6 1.0
CD C:GLU223 4.7 22.2 1.0
C17 C:LA3803 4.7 26.4 1.0
CE C:MET240 4.8 25.0 1.0
C5 C:LA3803 4.9 25.4 1.0

Zinc binding site 7 out of 8 in 3ljz

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Zinc binding site 7 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn998

b:12.9
occ:1.00
 OD2 D:ASP174 2.0 11.5 1.0
ND1 D:HIS200 2.0 13.2 1.0
NE2 D:HIS187 2.0 11.4 1.0
NE2 D:HIS172 2.1 12.8 1.0
CG D:ASP174 2.9 14.0 1.0
CE1 D:HIS187 3.0 12.6 1.0
CD2 D:HIS172 3.0 12.3 1.0
CE1 D:HIS200 3.0 14.5 1.0
CG D:HIS200 3.0 11.1 1.0
CD2 D:HIS187 3.1 11.2 1.0
CE1 D:HIS172 3.1 13.1 1.0
OD1 D:ASP174 3.1 11.3 1.0
CB D:HIS200 3.4 11.1 1.0
NE2 D:HIS200 4.1 12.8 1.0
ND1 D:HIS187 4.1 9.3 1.0
CG D:HIS172 4.1 10.6 1.0
ND1 D:HIS172 4.1 11.5 1.0
CD2 D:HIS200 4.1 13.8 1.0
CG D:HIS187 4.2 11.9 1.0
CB D:ASP174 4.3 14.2 1.0
O D:TYR176 4.4 13.6 1.0
CE1 D:PHE189 4.5 23.4 1.0
CZ D:PHE178 4.6 12.6 1.0
O D:HOH15 4.7 15.1 1.0
CZ D:PHE189 4.7 25.3 1.0
CE2 D:PHE178 4.8 12.6 1.0
CA D:HIS200 4.9 10.4 1.0
O D:HOH276 4.9 15.1 1.0

Zinc binding site 8 out of 8 in 3ljz

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Zinc binding site 8 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn999

b:16.4
occ:1.00
 NE2 D:HIS226 2.0 14.3 1.0
NE2 D:HIS232 2.0 15.6 1.0
NE2 D:HIS222 2.1 10.5 1.0
O21 D:LA3804 2.2 24.5 1.0
O23 D:LA3804 2.3 24.5 1.0
C20 D:LA3804 2.9 25.9 1.0
CD2 D:HIS232 3.0 18.9 1.0
CE1 D:HIS226 3.0 17.0 1.0
CE1 D:HIS232 3.0 19.0 1.0
CD2 D:HIS226 3.0 14.2 1.0
CD2 D:HIS222 3.0 11.5 1.0
CE1 D:HIS222 3.1 14.7 1.0
N22 D:LA3804 3.1 27.0 1.0
O D:HOH26 4.1 9.7 1.0
ND1 D:HIS232 4.1 20.4 1.0
ND1 D:HIS226 4.1 16.8 1.0
CG D:HIS232 4.1 19.8 1.0
CG D:HIS226 4.1 14.0 1.0
ND1 D:HIS222 4.2 13.0 1.0
CG D:HIS222 4.2 13.4 1.0
C19 D:LA3804 4.3 21.8 1.0
OE2 D:GLU223 4.4 21.2 1.0
OE1 D:GLU223 4.5 16.7 1.0
O D:HOH307 4.5 21.9 1.0
C8 D:LA3804 4.6 19.6 1.0
C17 D:LA3804 4.6 21.4 1.0
CE D:MET240 4.7 17.6 1.0
C4 D:LA3804 4.7 19.5 1.0
CD D:GLU223 4.8 17.3 1.0
C5 D:LA3804 4.9 18.4 1.0

Reference:

H.S.Shieh, A.G.Tomasselli, K.J.Mathis, M.E.Schnute, S.S.Woodard, N.Caspers, J.M.Williams, J.R.Kiefer, G.Munie, A.Wittwer, A.M.Malfait, M.D.Tortorella. Structure Analysis Reveals the Flexibility of the Adamts-5 Active Site. Protein Sci. V. 20 735 2011.
ISSN: ISSN 0961-8368
PubMed: 21370305
DOI: 10.1002/PRO.606
Page generated: Sat Oct 26 08:41:04 2024

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