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Zinc in PDB 1eak: Catalytic Domain of Prommp-2 E404Q Mutant

Enzymatic activity of Catalytic Domain of Prommp-2 E404Q Mutant

All present enzymatic activity of Catalytic Domain of Prommp-2 E404Q Mutant:
3.4.24.24;

Protein crystallography data

The structure of Catalytic Domain of Prommp-2 E404Q Mutant, PDB code: 1eak was solved by U.Bergmann, A.Tuuttila, K.Tryggvason, E.Morgunova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.58 / 2.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.670, 166.150, 170.130, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 30.3

Other elements in 1eak:

The structure of Catalytic Domain of Prommp-2 E404Q Mutant also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Prommp-2 E404Q Mutant (pdb code 1eak). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Catalytic Domain of Prommp-2 E404Q Mutant, PDB code: 1eak:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1eak

Go back to Zinc Binding Sites List in 1eak
Zinc binding site 1 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn996

b:26.5
occ:1.00
 NE2 A:HIS178 1.9 20.8 1.0
NE2 A:HIS193 2.1 37.8 1.0
ND1 A:HIS206 2.2 19.5 1.0
CE1 A:HIS193 2.4 31.7 1.0
OD2 A:ASP180 2.5 24.9 1.0
CD2 A:HIS178 2.8 23.5 1.0
CE1 A:HIS178 3.0 22.0 1.0
CG A:HIS206 3.0 21.3 1.0
CE1 A:HIS206 3.1 22.8 1.0
CG A:ASP180 3.2 25.5 1.0
OD1 A:ASP180 3.3 23.4 1.0
CB A:HIS206 3.3 18.3 1.0
CD2 A:HIS193 3.4 35.9 1.0
ND1 A:HIS193 3.7 27.4 1.0
CG A:HIS178 4.0 23.4 1.0
ND1 A:HIS178 4.0 21.6 1.0
CD2 A:HIS206 4.1 25.0 1.0
NE2 A:HIS206 4.2 27.4 1.0
CG A:HIS193 4.2 29.6 1.0
CE1 A:PHE195 4.2 27.9 1.0
CZ A:PHE195 4.4 26.7 1.0
O A:TYR182 4.5 25.9 1.0
CB A:ASP180 4.6 24.5 1.0
CA A:HIS206 4.8 19.4 1.0
CZ A:PHE184 4.9 15.0 1.0

Zinc binding site 2 out of 8 in 1eak

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Zinc binding site 2 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn997

b:20.3
occ:1.00
 NE2 A:HIS413 2.4 40.3 1.0
NE2 A:HIS403 2.4 34.1 1.0
NE2 A:HIS407 2.5 32.7 1.0
SG A:CYS102 2.5 24.4 1.0
CD2 A:HIS403 2.9 34.1 1.0
CD2 A:HIS413 3.1 40.2 1.0
CB A:CYS102 3.1 22.2 1.0
CD2 A:HIS407 3.2 33.2 1.0
CE1 A:HIS413 3.5 42.5 1.0
CE1 A:HIS407 3.6 34.6 1.0
CE1 A:HIS403 3.7 38.3 1.0
CB A:ASN104 4.1 28.0 1.0
CG A:HIS403 4.2 34.2 1.0
NE2 A:GLN404 4.3 28.7 1.0
CG A:HIS413 4.3 40.7 1.0
CG A:HIS407 4.4 31.1 1.0
ND1 A:HIS413 4.5 42.8 1.0
ND1 A:HIS407 4.5 34.4 1.0
ND1 A:HIS403 4.6 37.5 1.0
CA A:CYS102 4.6 22.2 1.0
CG A:ASN104 4.7 30.0 1.0
N A:ASN104 4.8 24.9 1.0
OE1 A:GLN404 5.0 28.4 1.0
CD A:GLN404 5.0 28.7 1.0
CA A:ASN104 5.0 25.7 1.0

Zinc binding site 3 out of 8 in 1eak

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Zinc binding site 3 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn996

b:24.4
occ:1.00
 NE2 B:HIS193 2.1 25.5 1.0
OD2 B:ASP180 2.3 26.8 1.0
NE2 B:HIS178 2.4 19.6 1.0
ND1 B:HIS206 2.4 27.2 1.0
CE1 B:HIS193 2.7 23.8 1.0
OD1 B:ASP180 3.0 26.0 1.0
CG B:ASP180 3.0 26.5 1.0
CD2 B:HIS178 3.2 21.0 1.0
CE1 B:HIS178 3.3 20.4 1.0
CG B:HIS206 3.3 27.9 1.0
CE1 B:HIS206 3.3 30.4 1.0
CD2 B:HIS193 3.4 26.6 1.0
CB B:HIS206 3.6 24.6 1.0
ND1 B:HIS193 3.9 22.7 1.0
O B:TYR182 4.1 24.4 1.0
CG B:HIS178 4.2 20.4 1.0
ND1 B:HIS178 4.2 21.6 1.0
CG B:HIS193 4.3 23.1 1.0
NE2 B:HIS206 4.3 34.7 1.0
CD2 B:HIS206 4.4 31.8 1.0
CE1 B:PHE195 4.4 25.2 1.0
CB B:ASP180 4.5 25.6 1.0
CZ B:PHE184 4.5 21.4 1.0
CZ B:PHE195 4.7 27.3 1.0
CE1 B:PHE184 4.7 21.4 1.0

Zinc binding site 4 out of 8 in 1eak

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Zinc binding site 4 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn997

b:23.2
occ:1.00
 NE2 B:HIS413 2.3 40.7 1.0
SG B:CYS102 2.4 25.5 1.0
NE2 B:HIS403 2.4 26.0 1.0
NE2 B:HIS407 2.4 22.5 1.0
CD2 B:HIS403 2.9 25.9 1.0
CD2 B:HIS413 3.1 40.2 1.0
CD2 B:HIS407 3.2 24.9 1.0
CE1 B:HIS407 3.2 24.7 1.0
CB B:CYS102 3.2 17.7 1.0
CE1 B:HIS413 3.3 41.8 1.0
CE1 B:HIS403 3.7 27.7 1.0
CB B:ASN104 3.7 26.0 1.0
ND1 B:HIS407 4.1 26.5 1.0
CG B:HIS407 4.1 24.5 1.0
CG B:HIS413 4.2 38.2 1.0
CG B:HIS403 4.2 25.5 1.0
ND1 B:HIS413 4.3 40.1 1.0
CG B:ASN104 4.4 25.6 1.0
NE2 B:GLN404 4.5 33.1 1.0
ND1 B:HIS403 4.5 27.4 1.0
CA B:CYS102 4.6 18.5 1.0
OD1 B:ASN104 4.8 22.1 1.0
OE1 B:GLN404 4.8 33.6 1.0
N B:ASN104 4.9 23.4 1.0
CA B:ASN104 4.9 25.0 1.0
ND2 B:ASN104 5.0 26.2 1.0
CD B:GLN404 5.0 32.5 1.0

Zinc binding site 5 out of 8 in 1eak

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Zinc binding site 5 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn996

b:32.1
occ:1.00
 NE2 C:HIS193 1.9 30.7 1.0
ND1 C:HIS206 2.3 24.1 1.0
OD2 C:ASP180 2.4 29.6 1.0
NE2 C:HIS178 2.5 27.1 1.0
CE1 C:HIS193 2.5 30.5 1.0
CD2 C:HIS178 3.0 28.2 1.0
CG C:ASP180 3.0 30.8 1.0
CD2 C:HIS193 3.1 32.1 1.0
CG C:HIS206 3.2 24.7 1.0
CE1 C:HIS206 3.2 28.6 1.0
OD1 C:ASP180 3.3 31.9 1.0
CE1 C:HIS178 3.3 26.3 1.0
CB C:HIS206 3.5 23.0 1.0
ND1 C:HIS193 3.7 29.1 1.0
CG C:HIS178 4.0 25.5 1.0
CG C:HIS193 4.0 28.7 1.0
ND1 C:HIS178 4.1 26.9 1.0
O C:TYR182 4.2 27.4 1.0
CD2 C:HIS206 4.3 28.4 1.0
NE2 C:HIS206 4.3 29.1 1.0
CB C:ASP180 4.3 29.1 1.0
CE2 C:PHE195 4.6 24.7 1.0
CZ C:PHE184 4.7 24.5 1.0
CZ C:PHE195 4.7 25.1 1.0
CA C:HIS206 4.9 22.2 1.0
CE2 C:PHE184 5.0 26.2 1.0

Zinc binding site 6 out of 8 in 1eak

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Zinc binding site 6 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn997

b:26.6
occ:1.00
 NE2 C:HIS413 2.4 44.2 1.0
SG C:CYS102 2.4 31.7 1.0
NE2 C:HIS403 2.4 41.7 1.0
NE2 C:HIS407 2.5 37.9 1.0
CD2 C:HIS413 3.1 43.9 1.0
CD2 C:HIS403 3.1 41.6 1.0
CD2 C:HIS407 3.1 37.4 1.0
CB C:CYS102 3.2 29.1 1.0
CE1 C:HIS413 3.3 46.4 1.0
CE1 C:HIS403 3.3 44.0 1.0
CE1 C:HIS407 3.4 39.6 1.0
CB C:ASN104 3.8 33.9 1.0
CG C:ASN104 4.1 35.5 1.0
CG C:HIS413 4.2 44.9 1.0
CG C:HIS403 4.2 40.7 1.0
ND1 C:HIS413 4.3 46.1 1.0
CG C:HIS407 4.3 37.9 1.0
ND1 C:HIS403 4.3 43.7 1.0
NE2 C:GLN404 4.3 34.2 1.0
ND1 C:HIS407 4.4 39.2 1.0
OD1 C:ASN104 4.6 36.0 1.0
ND2 C:ASN104 4.6 38.0 1.0
N C:ASN104 4.6 26.9 1.0
CA C:CYS102 4.6 29.4 1.0
CA C:ASN104 4.8 30.7 1.0
OE1 C:GLN404 4.8 37.2 1.0
CD C:GLN404 5.0 36.2 1.0
C C:CYS102 5.0 29.0 1.0

Zinc binding site 7 out of 8 in 1eak

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Zinc binding site 7 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn996

b:35.4
occ:1.00
 NE2 D:HIS193 2.1 33.1 1.0
OD2 D:ASP180 2.3 56.5 1.0
NE2 D:HIS178 2.4 36.1 1.0
ND1 D:HIS206 2.4 37.5 1.0
CD2 D:HIS178 2.7 36.6 1.0
CD2 D:HIS193 2.9 34.0 1.0
CE1 D:HIS193 3.2 33.7 1.0
CG D:ASP180 3.2 53.9 1.0
CE1 D:HIS178 3.2 37.2 1.0
CE1 D:HIS206 3.3 39.0 1.0
CG D:HIS206 3.4 40.6 1.0
CB D:ASP180 3.6 51.0 1.0
CG D:HIS178 3.6 36.2 1.0
CB D:HIS206 3.6 40.1 1.0
ND1 D:HIS178 3.8 36.3 1.0
O D:TYR182 4.1 36.9 1.0
CG D:HIS193 4.1 33.1 1.0
ND1 D:HIS193 4.2 32.9 1.0
OD1 D:ASP180 4.3 57.4 1.0
CE1 D:PHE195 4.4 40.6 1.0
NE2 D:HIS206 4.4 42.8 1.0
CD2 D:HIS206 4.5 42.6 1.0
CZ D:PHE195 4.6 39.4 1.0
CB D:HIS178 4.8 36.9 1.0
CZ D:PHE184 4.8 35.6 1.0
CB D:TYR182 4.9 37.8 1.0

Zinc binding site 8 out of 8 in 1eak

Go back to Zinc Binding Sites List in 1eak
Zinc binding site 8 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn997

b:40.1
occ:1.00
 NE2 D:HIS403 2.5 49.8 1.0
NE2 D:HIS413 2.5 56.9 1.0
NE2 D:HIS407 2.6 35.3 1.0
SG D:CYS102 2.7 50.0 1.0
CD2 D:HIS407 3.0 38.4 1.0
CD2 D:HIS403 3.1 48.9 1.0
CD2 D:HIS413 3.3 57.5 1.0
CB D:CYS102 3.3 40.7 1.0
CE1 D:HIS413 3.3 58.3 1.0
CE1 D:HIS403 3.4 50.6 1.0
CE1 D:HIS407 3.8 37.0 1.0
CB D:ASN104 3.9 44.4 1.0
ND1 D:HIS413 4.2 59.2 1.0
CG D:HIS403 4.2 48.9 1.0
CG D:HIS413 4.2 57.7 1.0
CG D:ASN104 4.3 44.9 1.0
ND1 D:HIS403 4.3 50.5 1.0
CG D:HIS407 4.3 40.1 1.0
OD1 D:ASN104 4.3 45.2 1.0
NE2 D:GLN404 4.6 51.9 1.0
ND1 D:HIS407 4.7 39.6 1.0
CA D:CYS102 4.8 40.5 1.0
CE D:MET421 4.8 44.9 1.0
N D:ASN104 4.8 40.0 1.0
CA D:ASN104 4.9 42.2 1.0
OE1 D:GLN404 5.0 50.4 1.0

Reference:

U.Bergmann, A.Tuuttila, E.Morgunova, K.Tryggvason. Crystal Structure of Human Mmp-2 Reveals A New P To Be Published.
Page generated: Sun Oct 13 00:06:37 2024

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