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Zinc in PDB 3b2z: Crystal Structure of ADAMTS4 (Apo Form)

Enzymatic activity of Crystal Structure of ADAMTS4 (Apo Form)

All present enzymatic activity of Crystal Structure of ADAMTS4 (Apo Form):
3.4.24.82;

Protein crystallography data

The structure of Crystal Structure of ADAMTS4 (Apo Form), PDB code: 3b2z was solved by L.Mosyak, M.Stahl, W.Somers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.330, 84.315, 150.146, 90.00, 112.23, 90.00
R / Rfree (%) 25.4 / 31.2

Other elements in 3b2z:

The structure of Crystal Structure of ADAMTS4 (Apo Form) also contains other interesting chemical elements:

Calcium (Ca) 16 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ADAMTS4 (Apo Form) (pdb code 3b2z). 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 ADAMTS4 (Apo Form), PDB code: 3b2z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3b2z

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Zinc binding site 1 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:37.0
occ:1.00
 NE2 A:HIS361 1.8 30.3 1.0
NE2 A:HIS371 2.1 35.0 1.0
NE2 A:HIS365 2.1 31.9 1.0
OD1 A:ASP328 2.2 55.1 1.0
OD2 A:ASP328 2.3 56.0 1.0
CG A:ASP328 2.4 55.9 1.0
CE1 A:HIS361 2.7 30.4 1.0
CD2 A:HIS371 2.9 36.9 1.0
CD2 A:HIS361 2.9 31.5 1.0
CD2 A:HIS365 3.0 33.2 1.0
CE1 A:HIS371 3.2 35.9 1.0
CE1 A:HIS365 3.3 31.6 1.0
CB A:ASP328 3.7 56.4 1.0
ND1 A:HIS361 3.9 31.8 1.0
CG A:HIS361 3.9 33.7 1.0
CG A:HIS371 4.1 37.8 1.0
CG A:HIS365 4.2 34.9 1.0
ND1 A:HIS371 4.2 36.5 1.0
ND1 A:HIS365 4.3 33.4 1.0
CE A:MET391 4.6 36.0 1.0
CA A:ASP328 4.7 56.2 1.0
OE1 A:GLN362 4.7 40.6 1.0
O A:HOH555 4.8 10.6 1.0
C A:ASP328 4.8 56.1 1.0

Zinc binding site 2 out of 8 in 3b2z

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Zinc binding site 2 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:37.0
occ:1.00
 NE2 B:HIS371 2.0 35.8 1.0
NE2 B:HIS365 2.1 37.6 1.0
NE2 B:HIS361 2.1 30.8 1.0
OD1 B:ASP328 2.2 51.0 1.0
OD2 B:ASP328 2.2 51.8 1.0
CG B:ASP328 2.4 52.4 1.0
CD2 B:HIS361 2.9 32.3 1.0
CE1 B:HIS371 3.0 35.5 1.0
CD2 B:HIS365 3.0 38.1 1.0
CD2 B:HIS371 3.0 35.6 1.0
CE1 B:HIS365 3.2 38.4 1.0
CE1 B:HIS361 3.3 31.2 1.0
CB B:ASP328 3.7 52.8 1.0
ND1 B:HIS371 4.1 35.5 1.0
CG B:HIS371 4.1 35.8 1.0
CG B:HIS361 4.1 34.8 1.0
CG B:HIS365 4.2 37.9 1.0
ND1 B:HIS365 4.2 38.3 1.0
ND1 B:HIS361 4.3 32.5 1.0
O B:ASP328 4.5 52.9 1.0
C B:ASP328 4.5 52.7 1.0
CE B:MET391 4.6 38.6 1.0
CA B:ASP328 4.6 52.9 1.0
OE1 B:GLN362 4.6 38.6 1.0
OG1 B:THR329 5.0 51.7 1.0

Zinc binding site 3 out of 8 in 3b2z

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Zinc binding site 3 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:39.0
occ:1.00
 NE2 C:HIS361 2.0 30.7 1.0
NE2 C:HIS371 2.0 34.9 1.0
NE2 C:HIS365 2.1 33.4 1.0
OD2 C:ASP328 2.3 62.4 1.0
OD1 C:ASP328 2.4 60.6 1.0
CG C:ASP328 2.6 62.7 1.0
CD2 C:HIS361 2.9 31.6 1.0
CD2 C:HIS371 2.9 35.9 1.0
CE1 C:HIS361 3.0 30.6 1.0
CE1 C:HIS365 3.1 33.5 1.0
CE1 C:HIS371 3.1 35.7 1.0
CD2 C:HIS365 3.1 34.0 1.0
CG C:HIS361 4.0 33.8 1.0
CB C:ASP328 4.1 63.6 1.0
ND1 C:HIS361 4.1 32.1 1.0
CG C:HIS371 4.1 37.3 1.0
ND1 C:HIS371 4.1 36.4 1.0
ND1 C:HIS365 4.2 33.7 1.0
CG C:HIS365 4.2 35.0 1.0
O C:HOH543 4.3 20.4 1.0
OG1 C:THR329 4.5 63.0 1.0
CE C:MET391 4.6 32.7 1.0
O C:ASP328 4.6 64.0 1.0
C C:ASP328 4.7 63.4 1.0
CA C:ASP328 4.8 63.5 1.0
NE2 C:GLN362 4.9 42.7 1.0

Zinc binding site 4 out of 8 in 3b2z

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Zinc binding site 4 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:32.9
occ:1.00
 NE2 D:HIS361 2.0 29.9 1.0
NE2 D:HIS365 2.0 34.1 1.0
NE2 D:HIS371 2.1 38.9 1.0
OD2 D:ASP328 2.4 47.0 1.0
OD1 D:ASP328 2.5 48.6 1.0
CG D:ASP328 2.7 49.3 1.0
CD2 D:HIS361 2.9 30.6 1.0
CE1 D:HIS365 2.9 36.0 1.0
CD2 D:HIS371 3.0 38.7 1.0
CE1 D:HIS361 3.0 30.7 1.0
CD2 D:HIS365 3.1 35.1 1.0
CE1 D:HIS371 3.1 38.2 1.0
CB D:ASP328 4.0 50.9 1.0
ND1 D:HIS361 4.1 31.6 1.0
CG D:HIS361 4.1 33.0 1.0
ND1 D:HIS365 4.1 36.9 1.0
CG D:HIS371 4.2 38.2 1.0
CG D:HIS365 4.2 35.0 1.0
ND1 D:HIS371 4.2 37.8 1.0
CE D:MET391 4.4 36.5 1.0
O D:ASP328 4.5 51.4 1.0
O D:HOH516 4.6 15.0 1.0
C D:ASP328 4.7 51.0 1.0
OG1 D:THR329 4.7 49.9 1.0
CA D:ASP328 4.8 50.9 1.0
OE1 D:GLN362 4.8 36.5 1.0

Zinc binding site 5 out of 8 in 3b2z

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Zinc binding site 5 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1

b:36.1
occ:1.00
 OD1 E:ASP328 2.0 57.5 1.0
NE2 E:HIS371 2.0 40.9 1.0
NE2 E:HIS361 2.1 32.6 1.0
NE2 E:HIS365 2.3 36.8 1.0
CG E:ASP328 2.6 57.1 1.0
OD2 E:ASP328 2.8 57.7 1.0
CE1 E:HIS371 2.8 40.8 1.0
CE1 E:HIS361 2.9 33.0 1.0
CD2 E:HIS365 3.0 36.8 1.0
CD2 E:HIS371 3.1 40.6 1.0
CD2 E:HIS361 3.2 32.2 1.0
CE1 E:HIS365 3.4 36.6 1.0
CB E:ASP328 4.0 56.8 1.0
ND1 E:HIS371 4.0 40.6 1.0
ND1 E:HIS361 4.0 32.2 1.0
CG E:HIS371 4.2 40.8 1.0
CG E:HIS361 4.2 32.0 1.0
CG E:HIS365 4.2 37.2 1.0
O E:ASP328 4.3 56.5 1.0
ND1 E:HIS365 4.4 36.9 1.0
C E:ASP328 4.6 56.4 1.0
CE E:MET391 4.6 38.3 1.0
CA E:ASP328 4.7 56.7 1.0
NE2 E:GLN362 4.7 32.0 1.0
OG1 E:THR329 4.8 55.9 1.0
O E:HOH529 4.9 20.4 1.0

Zinc binding site 6 out of 8 in 3b2z

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Zinc binding site 6 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1

b:34.4
occ:1.00
 NE2 F:HIS361 2.0 34.0 1.0
NE2 F:HIS371 2.0 37.5 1.0
NE2 F:HIS365 2.1 35.4 1.0
OD2 F:ASP328 2.3 50.6 1.0
OD1 F:ASP328 2.5 50.5 1.0
CG F:ASP328 2.7 50.4 1.0
CD2 F:HIS371 2.9 37.4 1.0
CD2 F:HIS361 2.9 34.4 1.0
CE1 F:HIS361 3.0 33.9 1.0
CD2 F:HIS365 3.0 35.6 1.0
CE1 F:HIS371 3.1 37.3 1.0
CE1 F:HIS365 3.1 35.5 1.0
CG F:HIS361 4.1 34.9 1.0
ND1 F:HIS361 4.1 34.1 1.0
CG F:HIS371 4.1 37.3 1.0
ND1 F:HIS371 4.1 37.2 1.0
CG F:HIS365 4.2 35.9 1.0
ND1 F:HIS365 4.2 35.6 1.0
CB F:ASP328 4.2 50.5 1.0
CE F:MET391 4.5 46.5 1.0
C F:ASP328 4.9 50.4 1.0
OG1 F:THR329 4.9 50.4 1.0
O F:ASP328 5.0 50.2 1.0

Zinc binding site 7 out of 8 in 3b2z

Go back to Zinc Binding Sites List in 3b2z
Zinc binding site 7 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1

b:41.5
occ:1.00
 NE2 G:HIS371 1.8 38.6 1.0
NE2 G:HIS361 1.9 36.0 1.0
NE2 G:HIS365 2.2 38.2 1.0
OD2 G:ASP328 2.4 57.5 1.0
OD1 G:ASP328 2.5 57.9 1.0
CD2 G:HIS371 2.7 38.6 1.0
CG G:ASP328 2.8 56.9 1.0
CE1 G:HIS361 2.9 35.7 1.0
CD2 G:HIS361 2.9 36.3 1.0
CE1 G:HIS371 3.0 38.5 1.0
CE1 G:HIS365 3.1 38.1 1.0
CD2 G:HIS365 3.2 37.9 1.0
CG G:HIS371 3.9 38.0 1.0
ND1 G:HIS361 4.0 36.1 1.0
ND1 G:HIS371 4.0 38.3 1.0
CG G:HIS361 4.0 36.8 1.0
ND1 G:HIS365 4.2 38.0 1.0
CB G:ASP328 4.2 57.2 1.0
CG G:HIS365 4.3 37.9 1.0
O G:ASP328 4.4 56.6 1.0
OG1 G:THR329 4.4 56.3 1.0
CE G:MET391 4.6 41.7 1.0
C G:ASP328 4.7 56.7 1.0
CA G:ASP328 5.0 57.0 1.0

Zinc binding site 8 out of 8 in 3b2z

Go back to Zinc Binding Sites List in 3b2z
Zinc binding site 8 out of 8 in the Crystal Structure of ADAMTS4 (Apo Form)


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 ADAMTS4 (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1

b:39.2
occ:1.00
 NE2 H:HIS371 2.1 39.5 1.0
NE2 H:HIS365 2.1 38.4 1.0
OD1 H:ASP328 2.3 55.0 1.0
NE2 H:HIS361 2.3 36.8 1.0
CG H:ASP328 2.6 55.2 1.0
OD2 H:ASP328 2.7 55.3 1.0
CD2 H:HIS361 2.8 36.8 1.0
CD2 H:HIS365 3.0 38.5 1.0
CE1 H:HIS371 3.1 39.3 1.0
CD2 H:HIS371 3.1 40.0 1.0
CE1 H:HIS365 3.1 38.4 1.0
CE1 H:HIS361 3.6 36.8 1.0
CB H:ASP328 3.9 55.2 1.0
CG H:HIS361 4.1 36.8 1.0
ND1 H:HIS371 4.2 39.5 1.0
CG H:HIS365 4.2 38.3 1.0
ND1 H:HIS365 4.2 38.4 1.0
CG H:HIS371 4.2 40.2 1.0
ND1 H:HIS361 4.4 36.7 1.0
O H:ASP328 4.5 55.0 1.0
C H:ASP328 4.6 55.1 1.0
OG1 H:THR329 4.6 54.7 1.0
CE H:MET391 4.7 59.8 1.0
NE2 H:GLN362 4.7 37.1 1.0
CA H:ASP328 4.7 55.3 1.0
OE1 H:GLN362 4.9 37.3 1.0

Reference:

L.Mosyak, K.Georgiadis, T.Shane, K.Svenson, T.Hebert, T.Mcdonagh, S.Mackie, S.Olland, L.Lin, X.Zhong, R.Kriz, E.L.Reifenberg, L.A.Collins-Racie, C.Corcoran, B.Freeman, R.Zollner, T.Marvell, M.Vera, P.E.Sum, E.R.Lavallie, M.Stahl, W.Somers. Crystal Structures of the Two Major Aggrecan Degrading Enzymes, ADAMTS4 and ADAMTS5. Protein Sci. V. 17 16 2008.
ISSN: ISSN 0961-8368
PubMed: 18042673
DOI: 10.1110/PS.073287008
Page generated: Thu Oct 24 11:22:58 2024

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