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Cadmium in PDB 1l4z: X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions

Enzymatic activity of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions

All present enzymatic activity of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions:
3.4.21.7;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions, PDB code: 1l4z was solved by N.Wakeham, S.Terzyan, P.Zhai, J.A.Loy, J.Tang, X.C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.400, 118.400, 134.900, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 26.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions (pdb code 1l4z). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions, PDB code: 1l4z:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1l4z

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Cadmium binding site 1 out of 6 in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd103

b:74.5
occ:0.50
 O A:HOH68 2.5 47.9 1.0
NE2 A:HIS569 2.5 46.9 1.0
CE1 A:HIS569 3.2 46.6 1.0
CD2 A:HIS569 3.7 46.0 1.0
CE A:LYS556 4.2 52.3 1.0
ND1 A:HIS569 4.4 46.2 1.0
CG A:HIS569 4.7 45.8 1.0
CG A:LYS556 4.7 51.1 1.0
CD A:LYS556 4.9 51.8 1.0
NZ A:LYS556 5.0 52.4 1.0

Cadmium binding site 2 out of 6 in 1l4z

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Cadmium binding site 2 out of 6 in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:76.9
occ:1.00
 OE1 A:GLU627 2.3 75.1 1.0
O A:HOH60 2.4 45.8 1.0
OE2 A:GLU627 2.5 76.3 1.0
NE2 A:HIS571 2.6 49.5 1.0
O A:HOH50 2.6 36.0 1.0
CD A:GLU627 2.7 76.0 1.0
O A:HOH7 3.2 41.4 1.0
CE1 A:HIS571 3.4 49.1 1.0
CD2 A:HIS571 3.6 48.8 1.0
CE1 A:HIS629 4.0 72.0 0.3
CG A:GLU627 4.1 76.3 1.0
ND1 A:HIS629 4.4 71.8 0.3
ND1 A:HIS571 4.6 48.9 1.0
CE A:LYS661 4.6 54.5 1.0
CB A:PRO570 4.7 45.3 1.0
CG A:HIS571 4.7 48.7 1.0
NE2 A:HIS629 4.8 72.0 0.3
CB A:GLU627 4.9 76.5 1.0

Cadmium binding site 3 out of 6 in 1l4z

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Cadmium binding site 3 out of 6 in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd105

b:74.5
occ:0.50
 CD A:CD106 2.4 68.6 0.5
O A:HOH2 2.6 48.3 1.0
OE2 A:GLU606 2.8 68.9 1.0
O A:HOH6 2.8 46.0 1.0
OE1 A:GLU606 3.2 69.1 1.0
NE2 A:HIS603 3.2 57.4 1.0
CE1 A:HIS603 3.2 57.5 1.0
CD A:GLU606 3.3 68.8 1.0
O A:HOH78 3.7 54.0 1.0
O A:HOH1 4.1 67.5 1.0
ND1 A:HIS603 4.4 56.8 1.0
CD2 A:HIS603 4.4 56.5 1.0
CG A:GLU606 4.7 68.1 1.0

Cadmium binding site 4 out of 6 in 1l4z

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Cadmium binding site 4 out of 6 in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd106

b:68.6
occ:0.50
 CD A:CD105 2.4 74.5 0.5
OE1 A:GLU606 2.5 69.1 1.0
NE2 A:HIS603 2.8 57.4 1.0
CD A:GLU606 3.4 68.8 1.0
OE2 A:GLU606 3.7 68.9 1.0
CE1 A:HIS603 3.8 57.5 1.0
CD2 A:HIS603 3.8 56.5 1.0
O A:HOH78 4.4 54.0 1.0
CZ2 A:TRP761 4.6 45.5 1.0
O A:HOH6 4.7 46.0 1.0
CG A:GLU606 4.8 68.1 1.0
NE1 A:TRP761 4.8 44.8 1.0
CE2 A:TRP761 4.9 45.3 1.0
ND1 A:HIS603 4.9 56.8 1.0
CG A:HIS603 4.9 56.1 1.0
O A:HOH2 5.0 48.3 1.0

Cadmium binding site 5 out of 6 in 1l4z

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Cadmium binding site 5 out of 6 in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:49.1
occ:1.00
 OD2 B:ASP32 2.1 45.4 1.0
NE2 B:HIS140 2.3 35.9 1.0
O B:HOH205 2.4 47.4 1.0
O B:HOH203 2.5 51.1 1.0
O B:HOH204 2.5 42.1 1.0
OD1 B:ASP32 2.6 46.5 1.0
CG B:ASP32 2.7 45.5 1.0
CE1 B:HIS140 3.0 35.1 1.0
CD2 B:HIS140 3.4 36.0 1.0
O B:HOH212 3.9 64.9 1.0
CB B:ASP32 4.2 45.7 1.0
ND1 B:HIS140 4.2 35.8 1.0
CG B:HIS140 4.5 36.7 1.0

Cadmium binding site 6 out of 6 in 1l4z

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Cadmium binding site 6 out of 6 in the X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Crystal Structure of the Complex of Microplasminogen with Alpha Domain of Streptokinase in the Presence Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:62.8
occ:1.00
 OG B:SER21 2.5 41.4 1.0
O B:HOH218 3.2 41.3 1.0
O B:HOH214 3.4 49.2 1.0
O B:HOH225 3.7 39.0 1.0
CB B:SER21 3.8 40.2 1.0
C B:SER21 4.0 39.5 1.0
CA B:SER21 4.1 40.0 1.0
O B:LEU35 4.1 47.5 1.0
O B:VAL22 4.1 38.7 1.0
N B:VAL22 4.3 38.8 1.0
O B:SER21 4.4 40.2 1.0
CD B:PRO4 4.4 49.6 1.0
CA B:GLY3 4.6 49.7 1.0
C B:VAL22 4.7 38.7 1.0
O B:HOH223 4.7 48.3 1.0
CB B:PHE37 4.9 50.8 1.0
CA B:VAL22 5.0 38.4 1.0

Reference:

N.Wakeham, S.Terzyan, P.Zhai, J.A.Loy, J.Tang, X.C.Zhang. Effects of Deletion of Streptokinase Residues 48-59 on Plasminogen Activation. Protein Eng. V. 15 753 2002.
ISSN: ISSN 0269-2139
PubMed: 12456874
DOI: 10.1093/PROTEIN/15.9.753
Page generated: Fri Jul 19 13:48:25 2024

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