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Cadmium in PDB 4a1i: Ykud From B.Subtilis

Protein crystallography data

The structure of Ykud From B.Subtilis, PDB code: 4a1i was solved by M.Blaise, S.Fuglsang Midtgaard, S.Roi Midtgaard, T.Boesen, S.Thirup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.302 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.450, 91.850, 123.700, 90.00, 90.25, 90.00
R / Rfree (%) 17.29 / 21.81

Other elements in 4a1i:

The structure of Ykud From B.Subtilis also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Ykud From B.Subtilis (pdb code 4a1i). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Ykud From B.Subtilis, PDB code: 4a1i:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4a1i

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Cadmium binding site 1 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1169

b:14.0
occ:0.82
O A:HOH2184 2.2 21.3 1.0
NE2 H:HIS119 2.3 9.3 1.0
SG A:CYS139 2.4 13.7 1.0
CL A:CL1170 2.5 17.4 1.0
O2 A:SO41165 2.6 18.5 1.0
O1 A:SO41165 2.7 12.2 0.9
CE1 H:HIS119 3.1 8.7 1.0
S A:SO41165 3.2 13.8 0.8
CB A:CYS139 3.3 13.2 1.0
CD2 H:HIS119 3.3 11.7 1.0
O A:HIS119 3.8 12.0 1.0
O4 A:SO41165 3.9 13.3 0.8
N A:CYS139 4.0 10.1 1.0
CA A:CYS139 4.2 11.1 1.0
ND1 H:HIS119 4.3 9.8 1.0
O3 A:SO41165 4.4 13.8 0.9
CG H:HIS119 4.4 10.2 1.0
CH2 A:TRP112 4.4 15.9 1.0
ND1 A:HIS119 4.4 11.3 1.0
NE2 A:HIS123 4.5 13.7 1.0
CZ3 A:TRP112 4.5 16.8 1.0
CE1 A:HIS119 4.7 12.0 1.0
CD2 A:HIS123 4.8 12.9 1.0
CB A:LYS137 4.8 15.4 1.0

Cadmium binding site 2 out of 8 in 4a1i

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Cadmium binding site 2 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1167

b:14.4
occ:0.83
O B:HOH2170 2.1 14.9 1.0
SG B:CYS139 2.4 13.3 1.0
CL B:CL1168 2.5 14.9 0.9
O4 B:SO41165 2.6 17.9 0.8
O3 B:SO41165 2.7 13.6 1.0
S B:SO41165 3.2 15.1 1.0
CB B:CYS139 3.3 13.1 1.0
O B:HIS119 3.8 9.7 1.0
O2 B:SO41165 3.9 15.3 1.0
N B:CYS139 4.0 10.0 1.0
CA B:CYS139 4.2 11.3 1.0
O1 B:SO41165 4.4 16.5 1.0
CH2 B:TRP112 4.5 16.0 1.0
ND1 B:HIS119 4.5 13.7 1.0
NE2 B:HIS123 4.5 13.9 1.0
CZ3 B:TRP112 4.5 16.3 1.0
CD2 B:HIS123 4.8 12.7 1.0
CE1 B:HIS119 4.8 13.6 1.0
C B:HIS119 5.0 10.2 1.0
CB B:LYS137 5.0 14.5 1.0

Cadmium binding site 3 out of 8 in 4a1i

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Cadmium binding site 3 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1168

b:15.0
occ:0.85
O C:HOH2173 2.2 16.0 1.0
NE2 F:HIS119 2.3 12.5 1.0
SG C:CYS139 2.4 13.8 1.0
CL C:CL1169 2.5 10.8 0.8
O2 C:SO41165 2.6 19.5 1.0
O4 C:SO41165 2.7 16.2 1.0
CE1 F:HIS119 3.1 11.8 1.0
S C:SO41165 3.2 17.2 1.0
CB C:CYS139 3.3 12.0 1.0
CD2 F:HIS119 3.4 13.5 1.0
O C:HIS119 3.9 14.6 1.0
O3 C:SO41165 4.0 20.2 1.0
N C:CYS139 4.0 10.2 1.0
CA C:CYS139 4.2 11.7 1.0
ND1 F:HIS119 4.3 11.1 1.0
O1 C:SO41165 4.4 18.0 1.0
CG F:HIS119 4.4 11.8 1.0
NE2 C:HIS123 4.5 12.5 1.0
CH2 C:TRP112 4.5 18.9 1.0
CZ3 C:TRP112 4.5 18.5 1.0
ND1 C:HIS119 4.5 11.6 1.0
O F:HOH2128 4.5 26.5 1.0
CE1 C:HIS119 4.7 13.3 1.0
CD2 C:HIS123 4.8 13.8 1.0
CB C:LYS137 4.9 13.9 1.0

Cadmium binding site 4 out of 8 in 4a1i

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Cadmium binding site 4 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1166

b:15.4
occ:0.86
O D:HOH2175 2.2 17.9 1.0
NE2 E:HIS119 2.3 11.1 1.0
SG D:CYS139 2.4 15.2 1.0
CL D:CL1167 2.5 17.3 1.0
O3 D:SO41165 2.6 15.8 0.9
O4 D:SO41165 2.8 14.7 1.0
CE1 E:HIS119 3.0 13.2 1.0
S D:SO41165 3.2 16.4 0.9
CB D:CYS139 3.3 15.3 1.0
CD2 E:HIS119 3.4 12.5 1.0
O D:HIS119 3.8 11.7 1.0
N D:CYS139 4.0 9.8 1.0
O1 D:SO41165 4.0 18.8 1.0
CA D:CYS139 4.2 11.7 1.0
ND1 E:HIS119 4.2 12.3 1.0
O2 D:SO41165 4.4 18.5 1.0
CG E:HIS119 4.4 11.6 1.0
ND1 D:HIS119 4.4 12.1 1.0
CH2 D:TRP112 4.5 13.4 1.0
NE2 D:HIS123 4.5 13.9 1.0
CZ3 D:TRP112 4.6 14.0 1.0
CE1 D:HIS119 4.7 14.3 1.0
CD2 D:HIS123 4.8 15.2 1.0
CB D:LYS137 4.8 17.8 1.0
O E:HOH2115 4.9 28.8 1.0
CE1 D:PHE108 4.9 23.4 1.0

Cadmium binding site 5 out of 8 in 4a1i

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Cadmium binding site 5 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd1168

b:14.7
occ:0.77
O E:HOH2144 2.0 9.1 1.0
NE2 D:HIS119 2.2 15.6 1.0
SG E:CYS139 2.4 13.7 1.0
CL E:CL1169 2.4 10.1 0.8
O1 E:SO41165 2.6 22.9 1.0
O4 E:SO41165 2.9 15.3 1.0
CE1 D:HIS119 2.9 14.3 1.0
S E:SO41165 3.3 14.7 1.0
CD2 D:HIS119 3.4 15.8 1.0
CB E:CYS139 3.4 10.6 1.0
O E:HIS119 3.9 12.5 1.0
N E:CYS139 4.1 8.9 1.0
O2 E:SO41165 4.1 14.1 1.0
ND1 D:HIS119 4.1 12.1 1.0
CA E:CYS139 4.3 10.8 1.0
NE2 E:HIS123 4.4 10.3 1.0
CH2 E:TRP112 4.4 17.4 1.0
CG D:HIS119 4.4 12.4 1.0
O3 E:SO41165 4.5 14.9 1.0
CZ3 E:TRP112 4.5 17.8 1.0
ND1 E:HIS119 4.5 12.3 1.0
O E:HOH2115 4.5 28.8 1.0
O E:HOH2169 4.5 37.4 1.0
CE1 E:HIS119 4.7 13.2 1.0
CD2 E:HIS123 4.7 11.2 1.0
CB E:LYS137 4.8 15.5 1.0

Cadmium binding site 6 out of 8 in 4a1i

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Cadmium binding site 6 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd1168

b:15.3
occ:0.82
O F:HOH2162 2.2 17.4 1.0
NE2 C:HIS119 2.3 13.8 1.0
SG F:CYS139 2.4 14.5 1.0
CL F:CL1169 2.5 16.8 0.9
O1 F:SO41165 2.6 18.6 1.0
O3 F:SO41165 2.7 14.6 1.0
CE1 C:HIS119 3.1 13.3 1.0
S F:SO41165 3.2 17.0 0.9
CB F:CYS139 3.3 17.8 1.0
CD2 C:HIS119 3.3 13.3 1.0
O F:HIS119 3.8 13.5 1.0
O4 F:SO41165 4.0 20.5 1.0
N F:CYS139 4.0 12.8 1.0
CA F:CYS139 4.2 13.2 1.0
ND1 C:HIS119 4.3 11.6 1.0
O2 F:SO41165 4.4 17.9 1.0
CG C:HIS119 4.4 11.1 1.0
ND1 F:HIS119 4.4 11.1 1.0
NE2 F:HIS123 4.5 16.6 1.0
CH2 F:TRP112 4.5 15.8 1.0
CZ3 F:TRP112 4.5 16.2 1.0
O F:HOH2192 4.6 38.6 1.0
CE1 F:HIS119 4.6 11.8 1.0
O F:HOH2128 4.6 26.5 1.0
CD2 F:HIS123 4.8 17.9 1.0
CB F:LYS137 4.9 19.5 1.0
CE1 F:PHE108 4.9 24.4 1.0

Cadmium binding site 7 out of 8 in 4a1i

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Cadmium binding site 7 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cd1168

b:13.3
occ:0.74
O G:HOH2133 2.0 9.6 1.0
SG G:CYS139 2.4 13.4 1.0
CL G:CL1169 2.5 15.4 0.9
O1 G:SO41165 2.6 17.1 1.0
O2 G:SO41165 2.7 7.6 0.9
S G:SO41165 3.2 11.3 0.9
CB G:CYS139 3.3 11.7 1.0
O G:HIS119 3.9 9.1 1.0
O3 G:SO41165 4.0 11.3 0.9
N G:CYS139 4.0 10.3 1.0
CA G:CYS139 4.2 8.8 1.0
NE2 G:HIS123 4.3 11.7 1.0
O4 G:SO41165 4.4 10.8 0.9
CZ3 G:TRP112 4.4 15.4 1.0
CH2 G:TRP112 4.5 16.9 1.0
O G:HOH2102 4.5 26.7 1.0
ND1 G:HIS119 4.5 11.2 1.0
CD2 G:HIS123 4.7 13.4 1.0
CE1 G:HIS119 4.7 12.1 1.0
CB G:LYS137 4.8 14.2 1.0
O G:HOH2161 4.9 38.7 1.0
CE1 G:PHE108 5.0 25.0 1.0

Cadmium binding site 8 out of 8 in 4a1i

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Cadmium binding site 8 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Ykud From B.Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd1168

b:15.5
occ:0.84
O H:HOH2136 2.2 14.8 1.0
NE2 A:HIS119 2.2 12.4 1.0
SG H:CYS139 2.4 14.9 1.0
CL H:CL1169 2.6 9.2 0.7
O1 H:SO41165 2.7 13.6 0.7
O2 H:SO41165 2.7 15.7 1.0
CE1 A:HIS119 3.1 12.0 1.0
S H:SO41165 3.2 13.7 0.9
CB H:CYS139 3.3 12.9 1.0
CD2 A:HIS119 3.3 11.6 1.0
O H:HIS119 3.9 9.8 1.0
N H:CYS139 4.0 11.8 1.0
O3 H:SO41165 4.0 14.6 0.8
CA H:CYS139 4.2 11.0 1.0
ND1 A:HIS119 4.2 11.3 1.0
O4 H:SO41165 4.4 12.2 0.8
CG A:HIS119 4.4 10.1 1.0
CH2 H:TRP112 4.4 14.9 1.0
NE2 H:HIS123 4.4 12.0 1.0
ND1 H:HIS119 4.4 9.8 1.0
CZ3 H:TRP112 4.5 16.8 1.0
CE1 H:HIS119 4.6 8.7 1.0
CD2 H:HIS123 4.8 12.1 1.0
CB H:LYS137 4.8 18.1 1.0

Reference:

M.Blaise, S.Fuglsang Midtgaard, S.Roi Midtgaard, T.Boesen, S.Thirup. Structures of Three New Crystal Forms of the Ykud L,D-Transpeptidase From B. Subtilis. To Be Published.
Page generated: Fri Jul 19 16:53:41 2024

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