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Calcium in PDB 7ed1: Transferase From Mycobacterium Tuberculosis

Protein crystallography data

The structure of Transferase From Mycobacterium Tuberculosis, PDB code: 7ed1 was solved by D.-G.Kim, B.-J.Lee, S.J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.45 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.559, 73.858, 65.196, 90, 94.73, 90
R / Rfree (%) 18.2 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Transferase From Mycobacterium Tuberculosis (pdb code 7ed1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Transferase From Mycobacterium Tuberculosis, PDB code: 7ed1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7ed1

Go back to Calcium Binding Sites List in 7ed1
Calcium binding site 1 out of 6 in the Transferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Transferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:11.6
occ:1.00
 O A:HOH481 2.3 15.9 1.0
O A:HOH593 2.4 20.6 1.0
O1A A:COA301 2.4 12.3 1.0
O5A A:COA301 2.4 13.2 1.0
O A:HOH548 2.5 17.0 1.0
O A:HOH519 2.5 22.3 1.0
O A:HOH443 2.5 12.4 1.0
P1A A:COA301 3.6 12.8 1.0
P2A A:COA301 3.7 13.5 1.0
O3A A:COA301 3.9 11.6 1.0
O A:HOH425 4.1 17.7 1.0
O A:HOH493 4.3 13.9 1.0
ND1 A:HIS88 4.4 10.0 1.0
CE1 A:HIS88 4.4 10.9 1.0
O A:HIS88 4.5 11.5 1.0
O A:HOH513 4.5 15.0 1.0
O4A A:COA301 4.5 12.3 1.0
C5B A:COA301 4.6 10.7 1.0
O B:HOH571 4.6 28.4 1.0
OE2 A:GLU46 4.6 16.5 1.0
O5B A:COA301 4.7 11.6 1.0
O2A A:COA301 4.7 12.5 1.0
O A:HOH525 4.7 15.6 1.0
OE1 A:GLU46 4.7 14.0 1.0
O B:HOH554 4.8 7.3 1.0
O6A A:COA301 4.9 14.4 1.0

Calcium binding site 2 out of 6 in 7ed1

Go back to Calcium Binding Sites List in 7ed1
Calcium binding site 2 out of 6 in the Transferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Transferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:13.3
occ:1.00
 O A:HOH493 2.4 13.9 1.0
OE2 A:GLU111 2.4 13.7 1.0
O A:ALA110 2.4 12.2 1.0
OD1 A:ASP109 2.4 12.2 1.0
OD2 A:ASP109 2.5 11.9 1.0
O4A A:COA301 2.5 12.3 1.0
CG A:ASP109 2.7 12.3 1.0
O2A A:COA301 3.2 12.5 1.0
CD A:GLU111 3.4 15.0 1.0
O3A A:COA301 3.5 11.6 1.0
P2A A:COA301 3.6 13.5 1.0
C A:ALA110 3.6 12.2 1.0
CG A:GLU111 3.9 13.8 1.0
P1A A:COA301 3.9 12.8 1.0
N A:ALA110 4.0 11.3 1.0
O A:HOH525 4.1 15.6 1.0
OG1 A:THR87 4.1 10.9 1.0
CB A:ASP109 4.2 12.7 1.0
N A:GLU111 4.4 13.4 1.0
CA A:ALA110 4.5 11.1 1.0
OE1 A:GLU111 4.5 15.0 1.0
O5A A:COA301 4.5 13.2 1.0
O A:HOH590 4.5 24.0 1.0
O6A A:COA301 4.6 14.4 1.0
CA A:GLU111 4.6 13.2 1.0
O1A A:COA301 4.7 12.3 1.0
O A:HIS88 4.7 11.5 1.0
CA A:ASP109 4.8 11.3 1.0
C A:ASP109 4.8 12.2 1.0
O A:HOH519 4.8 22.3 1.0
CG A:GLU151 4.9 14.1 1.0
CB A:GLU151 4.9 13.5 1.0
CB A:GLU111 4.9 14.1 1.0
CB A:CYS89 4.9 12.4 1.0
O A:HOH412 5.0 22.9 1.0

Calcium binding site 3 out of 6 in 7ed1

Go back to Calcium Binding Sites List in 7ed1
Calcium binding site 3 out of 6 in the Transferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Transferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:13.8
occ:1.00
 O A:SER16 2.2 12.1 1.0
O A:HOH543 2.3 13.9 1.0
OE1 A:GLU60 2.4 17.9 1.0
O A:HOH487 2.5 16.1 1.0
O A:HOH561 2.5 15.7 1.0
OD2 A:ASP3 2.6 18.9 1.0
OE2 A:GLU60 2.7 19.9 1.0
OD1 A:ASP3 2.8 19.8 1.0
CD A:GLU60 2.9 17.4 1.0
CG A:ASP3 3.0 19.4 1.0
C A:SER16 3.5 12.4 1.0
N A:SER16 4.1 12.7 1.0
CA A:SER16 4.4 12.2 1.0
N A:ALA17 4.4 11.9 1.0
CG A:GLU60 4.4 19.1 1.0
OG A:SER16 4.4 13.1 1.0
O A:HOH533 4.4 30.5 1.0
O A:HOH405 4.5 22.9 1.0
O A:HOH403 4.5 38.4 1.0
CB A:ASP3 4.5 17.9 1.0
CA A:ALA17 4.5 12.7 1.0
O A:HOH410 4.6 24.9 1.0
O A:HOH447 4.7 15.3 1.0
CB A:ALA17 4.8 13.7 1.0
O A:HOH586 4.8 46.0 1.0

Calcium binding site 4 out of 6 in 7ed1

Go back to Calcium Binding Sites List in 7ed1
Calcium binding site 4 out of 6 in the Transferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Transferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:12.8
occ:1.00
 O B:HOH453 2.3 15.0 1.0
O2A B:COA301 2.4 12.0 1.0
O B:HOH567 2.4 21.0 1.0
O4A B:COA301 2.5 13.8 1.0
O B:HOH525 2.5 18.2 1.0
O B:HOH433 2.5 14.6 1.0
O B:HOH540 2.5 21.6 1.0
P1A B:COA301 3.6 12.5 1.0
P2A B:COA301 3.7 14.1 1.0
O3A B:COA301 3.9 13.2 1.0
O B:HOH449 4.0 17.5 1.0
O B:HOH489 4.3 15.7 1.0
ND1 B:HIS88 4.4 12.2 1.0
CE1 B:HIS88 4.4 12.1 1.0
O B:HIS88 4.4 13.0 1.0
O5A B:COA301 4.5 14.3 1.0
O B:HOH445 4.5 13.3 1.0
OE2 B:GLU46 4.6 16.8 1.0
C5B B:COA301 4.6 12.4 1.0
O1A B:COA301 4.6 14.2 1.0
O B:HOH475 4.7 17.9 1.0
O5B B:COA301 4.7 11.9 1.0
OE1 B:GLU46 4.7 14.8 1.0
O A:HOH598 4.7 26.6 1.0
O B:HOH565 4.8 7.9 1.0
O6A B:COA301 4.9 13.7 1.0
O B:HOH568 4.9 33.8 1.0

Calcium binding site 5 out of 6 in 7ed1

Go back to Calcium Binding Sites List in 7ed1
Calcium binding site 5 out of 6 in the Transferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Transferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:16.4
occ:1.00
 O B:HOH489 2.3 15.7 1.0
OE2 B:GLU111 2.4 14.6 1.0
OD1 B:ASP109 2.4 13.7 1.0
O5A B:COA301 2.4 14.3 1.0
O B:ALA110 2.5 13.1 1.0
OD2 B:ASP109 2.5 13.4 1.0
CG B:ASP109 2.8 13.6 1.0
O1A B:COA301 3.1 14.2 1.0
CD B:GLU111 3.4 15.8 1.0
P2A B:COA301 3.5 14.1 1.0
O3A B:COA301 3.6 13.2 1.0
C B:ALA110 3.7 13.9 1.0
CG B:GLU111 3.9 15.0 1.0
P1A B:COA301 3.9 12.5 1.0
O B:HOH475 4.0 17.9 1.0
N B:ALA110 4.1 11.9 1.0
OG1 B:THR87 4.1 10.9 1.0
CB B:ASP109 4.3 13.1 1.0
OE1 B:GLU111 4.5 16.1 1.0
O4A B:COA301 4.5 13.8 1.0
N B:GLU111 4.5 14.3 1.0
CA B:ALA110 4.5 12.3 1.0
O6A B:COA301 4.6 13.7 1.0
O2A B:COA301 4.7 12.0 1.0
CA B:GLU111 4.7 14.9 1.0
O B:HIS88 4.8 13.0 1.0
CA B:ASP109 4.8 12.5 1.0
O B:HOH540 4.8 21.6 1.0
C B:ASP109 4.9 12.3 1.0
CG B:GLU151 4.9 16.9 1.0
CB B:GLU151 4.9 15.2 1.0
CB B:GLU111 4.9 14.8 1.0
CB B:CYS89 4.9 12.9 1.0
NZ B:LYS155 5.0 12.5 1.0

Calcium binding site 6 out of 6 in 7ed1

Go back to Calcium Binding Sites List in 7ed1
Calcium binding site 6 out of 6 in the Transferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Transferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:15.4
occ:1.00
 O B:SER16 2.3 14.3 1.0
O B:HOH523 2.3 16.3 1.0
OE1 B:GLU60 2.3 22.1 1.0
O B:HOH527 2.4 18.9 1.0
O B:HOH459 2.5 16.2 1.0
OD2 B:ASP3 2.5 21.3 1.0
OE2 B:GLU60 2.7 22.1 1.0
OD1 B:ASP3 2.8 19.6 1.0
CD B:GLU60 2.9 19.7 1.0
CG B:ASP3 3.0 19.6 1.0
C B:SER16 3.5 14.6 1.0
N B:SER16 4.1 14.2 1.0
CG B:GLU60 4.4 19.9 1.0
CA B:SER16 4.4 13.5 1.0
N B:ALA17 4.4 13.3 1.0
OG B:SER16 4.4 13.8 1.0
O B:HOH403 4.4 22.7 1.0
CB B:ASP3 4.5 18.5 1.0
CA B:ALA17 4.5 13.0 1.0
O B:HOH416 4.5 24.2 1.0
O B:HOH505 4.7 36.1 1.0
O B:HOH422 4.7 18.4 1.0
O B:HOH458 4.7 34.1 1.0
CB B:ALA17 4.7 13.5 1.0

Reference:

D.-G.Kim, B.-J.Lee, S.J.Lee. Transferase From Mycobacterium Tuberculosis To Be Published.
Page generated: Fri Jul 19 00:24:04 2024

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