Atomistry » Manganese » PDB 4ima-4k28 » 4irq
Atomistry »
  Manganese »
    PDB 4ima-4k28 »
      4irq »

Manganese in PDB 4irq: Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp

Enzymatic activity of Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp

All present enzymatic activity of Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp:
2.4.1.133;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp, PDB code: 4irq was solved by Y.Tsutsui, B.Ramakrishnan, P.K.Qasba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.85 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.122, 121.532, 97.137, 90.00, 95.12, 90.00
R / Rfree (%) 18.5 / 23.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp (pdb code 4irq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp, PDB code: 4irq:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4irq

Go back to Manganese Binding Sites List in 4irq
Manganese binding site 1 out of 4 in the Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:38.2
occ:1.00
 O1B A:UDP402 2.1 31.8 1.0
O1A A:UDP402 2.1 32.6 1.0
O A:HOH501 2.3 32.8 1.0
NE2 A:HIS257 2.3 36.4 1.0
OD2 A:ASP165 2.3 36.7 1.0
ND1 A:HIS259 2.4 39.0 1.0
CE1 A:HIS259 3.2 42.5 1.0
CE1 A:HIS257 3.2 38.0 1.0
CG A:ASP165 3.2 39.5 1.0
PB A:UDP402 3.3 40.3 1.0
PA A:UDP402 3.3 37.1 1.0
CD2 A:HIS257 3.4 40.0 1.0
OD1 A:ASP165 3.4 40.1 1.0
CG A:HIS259 3.5 40.7 1.0
O3A A:UDP402 3.7 31.8 1.0
O3B A:UDP402 3.8 34.6 1.0
CB A:HIS259 3.8 44.7 1.0
O2A A:UDP402 4.1 36.6 1.0
O A:HOH547 4.1 45.4 1.0
O A:HOH531 4.1 37.3 1.0
O3' A:UDP402 4.2 32.0 1.0
NH2 A:ARG266 4.2 37.2 1.0
NE2 A:HIS259 4.4 45.6 1.0
ND1 A:HIS257 4.4 34.5 1.0
CG A:HIS257 4.5 37.4 1.0
O2B A:UDP402 4.5 39.9 1.0
CD2 A:HIS259 4.5 40.1 1.0
O5' A:UDP402 4.5 33.5 1.0
CB A:ASP165 4.6 39.7 1.0
C3' A:UDP402 4.8 33.4 1.0
C5' A:UDP402 4.8 38.6 1.0

Manganese binding site 2 out of 4 in 4irq

Go back to Manganese Binding Sites List in 4irq
Manganese binding site 2 out of 4 in the Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:41.4
occ:1.00
 O1A B:UDP402 2.2 35.7 1.0
O1B B:UDP402 2.2 39.6 1.0
O B:HOH501 2.3 36.4 1.0
ND1 B:HIS259 2.3 40.6 1.0
NE2 B:HIS257 2.3 45.1 1.0
OD2 B:ASP165 2.4 34.3 1.0
CG B:ASP165 3.1 45.4 1.0
CE1 B:HIS259 3.1 38.1 1.0
CE1 B:HIS257 3.1 43.1 1.0
OD1 B:ASP165 3.2 41.2 1.0
CG B:HIS259 3.4 36.6 1.0
CD2 B:HIS257 3.4 42.8 1.0
PB B:UDP402 3.4 45.8 1.0
PA B:UDP402 3.5 41.2 1.0
CB B:HIS259 3.7 38.1 1.0
O3A B:UDP402 3.8 42.1 1.0
O3B B:UDP402 3.9 43.4 1.0
O3' B:UDP402 4.1 30.1 1.0
NH2 B:ARG266 4.3 38.2 1.0
O2A B:UDP402 4.3 44.2 1.0
NE2 B:HIS259 4.3 40.4 1.0
ND1 B:HIS257 4.3 46.9 1.0
O B:HOH560 4.4 40.9 1.0
CD2 B:HIS259 4.4 39.4 1.0
O B:HOH549 4.4 44.3 1.0
CG B:HIS257 4.5 46.8 1.0
CB B:ASP165 4.5 36.4 1.0
O5' B:UDP402 4.6 42.5 1.0
O2B B:UDP402 4.6 41.5 1.0
C3' B:UDP402 4.7 35.3 1.0
C5' B:UDP402 4.8 37.1 1.0

Manganese binding site 3 out of 4 in 4irq

Go back to Manganese Binding Sites List in 4irq
Manganese binding site 3 out of 4 in the Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:36.9
occ:1.00
 O1B C:UDP402 2.1 36.2 1.0
O1A C:UDP402 2.2 39.3 1.0
OD2 C:ASP165 2.3 41.4 1.0
ND1 C:HIS259 2.3 34.3 1.0
NE2 C:HIS257 2.3 39.0 1.0
O C:HOH501 2.5 33.1 1.0
CE1 C:HIS257 3.2 40.0 1.0
CG C:ASP165 3.2 40.4 1.0
CE1 C:HIS259 3.2 36.6 1.0
PB C:UDP402 3.3 41.0 1.0
CG C:HIS259 3.4 40.2 1.0
OD1 C:ASP165 3.4 37.6 1.0
PA C:UDP402 3.4 38.8 1.0
CD2 C:HIS257 3.4 37.7 1.0
O3A C:UDP402 3.7 32.6 1.0
CB C:HIS259 3.7 40.0 1.0
O3B C:UDP402 4.0 36.1 1.0
O3' C:UDP402 4.1 34.9 1.0
NH2 C:ARG266 4.1 28.4 1.0
O C:HOH517 4.2 37.2 1.0
O2A C:UDP402 4.2 36.5 1.0
ND1 C:HIS257 4.4 41.0 1.0
NH1 C:ARG104 4.4 33.0 0.4
NE2 C:HIS259 4.4 43.3 1.0
O2B C:UDP402 4.5 39.9 1.0
CD2 C:HIS259 4.5 42.2 1.0
CG C:HIS257 4.5 38.0 1.0
O5' C:UDP402 4.6 42.5 1.0
CB C:ASP165 4.6 37.9 1.0
C3' C:UDP402 4.7 36.8 1.0
O C:HOH533 4.9 40.2 1.0
C5' C:UDP402 4.9 33.2 1.0

Manganese binding site 4 out of 4 in 4irq

Go back to Manganese Binding Sites List in 4irq
Manganese binding site 4 out of 4 in the Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Catalytic Domain of Human BETA1, 4GALACTOSYLTRANSFERASE 7 in Closed Conformation in Complex with Manganese and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:33.5
occ:1.00
 O1A D:UDP402 2.2 27.4 1.0
O1B D:UDP402 2.2 34.3 1.0
NE2 D:HIS257 2.3 30.2 1.0
ND1 D:HIS259 2.3 33.8 1.0
OD2 D:ASP165 2.4 39.4 1.0
O D:HOH501 2.4 28.6 1.0
CE1 D:HIS257 3.1 40.0 1.0
CE1 D:HIS259 3.1 32.3 1.0
CG D:ASP165 3.2 35.6 1.0
OD1 D:ASP165 3.3 36.3 1.0
CD2 D:HIS257 3.3 39.3 1.0
PB D:UDP402 3.3 38.1 1.0
CG D:HIS259 3.4 33.3 1.0
PA D:UDP402 3.4 38.6 1.0
O3A D:UDP402 3.8 38.2 1.0
CB D:HIS259 3.8 35.7 1.0
O3B D:UDP402 3.9 36.1 1.0
O D:HOH536 4.2 34.7 1.0
O3' D:UDP402 4.2 34.5 1.0
NH2 D:ARG266 4.3 35.4 1.0
ND1 D:HIS257 4.3 42.6 1.0
O2A D:UDP402 4.3 37.0 1.0
NE2 D:HIS259 4.3 36.2 1.0
O D:HOH547 4.4 38.0 1.0
CG D:HIS257 4.4 37.5 1.0
O D:HOH545 4.5 40.4 1.0
CD2 D:HIS259 4.5 41.4 1.0
O2B D:UDP402 4.5 41.4 1.0
O5' D:UDP402 4.6 31.6 1.0
CB D:ASP165 4.6 44.5 1.0
C5' D:UDP402 4.7 34.9 1.0
C3' D:UDP402 4.8 27.8 1.0

Reference:

Y.Tsutsui, B.Ramakrishnan, P.K.Qasba. Crystal Structure of Human BETA1,4GALACTOSYLTRANSFERASE 7 in A Conformational Transition Show Re-Organization of the Binding Pocket To Be Published.
Page generated: Sat Oct 5 19:51:56 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy