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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

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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

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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

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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

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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

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