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Manganese in PDB 6vrs: Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations

Enzymatic activity of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations

All present enzymatic activity of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations:
5.3.1.5;

Manganese Binding Sites:

The binding sites of Manganese atom in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations (pdb code 6vrs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations, PDB code: 6vrs:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6vrs

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Manganese binding site 1 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:87.9
occ:1.00
 OD2 A:ASP255 2.4 84.0 1.0
OE2 A:GLU217 2.5 77.0 1.0
NE2 A:HIS220 2.5 66.0 1.0
OD1 A:ASP257 2.6 85.1 1.0
OE1 A:GLU217 3.0 71.1 1.0
CD A:GLU217 3.1 70.9 1.0
CG A:ASP255 3.1 76.4 1.0
OD1 A:ASP255 3.1 75.6 1.0
OD2 A:ASP257 3.2 89.8 1.0
CG A:ASP257 3.3 79.0 1.0
CE1 A:HIS220 3.3 61.6 1.0
CD2 A:HIS220 3.6 63.2 1.0
OD2 A:ASP287 3.9 89.7 1.0
O A:HOH503 3.9 51.2 1.0
MN A:MN402 4.3 91.6 1.0
ND1 A:HIS220 4.5 53.3 1.0
ND2 A:ASN247 4.5 54.0 1.0
CB A:ASP255 4.6 65.5 1.0
CG A:ASP287 4.6 82.5 1.0
CG A:GLU217 4.6 63.6 1.0
CG A:HIS220 4.6 57.6 1.0
NZ A:LYS183 4.7 56.6 1.0
CB A:ASP257 4.7 68.1 1.0
CE A:LYS183 4.9 50.4 1.0
OD1 A:ASP287 4.9 88.5 1.0

Manganese binding site 2 out of 8 in 6vrs

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Manganese binding site 2 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:91.6
occ:1.00
 OD2 A:ASP287 2.0 89.7 1.0
OE2 A:GLU181 2.1 0.5 1.0
OD2 A:ASP245 2.4 82.7 1.0
O A:HOH503 2.4 51.2 1.0
OE1 A:GLU217 2.4 71.1 1.0
O A:HOH502 2.5 81.2 1.0
CD A:GLU181 2.9 88.3 1.0
O A:HOH501 3.1 70.1 1.0
OE1 A:GLU181 3.2 91.2 1.0
CG A:ASP287 3.2 82.5 1.0
O A:HOH504 3.5 29.9 1.0
CG A:ASP245 3.6 80.6 1.0
CD A:GLU217 3.6 70.9 1.0
CB A:ASP287 3.9 72.0 1.0
CE1 A:HIS220 4.1 61.6 1.0
OD1 A:ASP287 4.2 88.5 1.0
MN A:MN401 4.3 87.9 1.0
CG A:GLU181 4.3 72.6 1.0
CB A:ASP245 4.4 72.5 1.0
OD1 A:ASP245 4.5 80.8 1.0
CG A:GLU217 4.5 63.6 1.0
OE2 A:GLU217 4.5 77.0 1.0
CB A:GLU217 4.6 54.2 1.0
NE2 A:HIS220 4.8 66.0 1.0
ND1 A:HIS220 4.9 53.3 1.0

Manganese binding site 3 out of 8 in 6vrs

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Manganese binding site 3 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:88.0
occ:1.00
 OD1 B:ASP255 2.4 86.0 1.0
OE2 B:GLU217 2.5 76.8 1.0
NE2 B:HIS220 2.5 67.2 1.0
OD1 B:ASP257 2.6 83.6 1.0
OE1 B:GLU217 3.0 74.7 1.0
CD B:GLU217 3.1 73.4 1.0
OD2 B:ASP257 3.1 82.4 1.0
OD2 B:ASP255 3.1 86.5 1.0
CG B:ASP255 3.2 79.1 1.0
CG B:ASP257 3.2 74.9 1.0
CE1 B:HIS220 3.3 61.7 1.0
CD2 B:HIS220 3.6 63.4 1.0
OD2 B:ASP287 3.9 91.9 1.0
O B:HOH503 4.0 57.6 1.0
MN B:MN402 4.2 89.7 1.0
ND1 B:HIS220 4.4 53.6 1.0
ND2 B:ASN247 4.5 55.2 1.0
CG B:ASP287 4.6 84.3 1.0
CG B:GLU217 4.6 65.6 1.0
CB B:ASP255 4.6 69.3 1.0
CG B:HIS220 4.6 57.0 1.0
NZ B:LYS183 4.7 55.6 1.0
CB B:ASP257 4.7 65.4 1.0
CE B:LYS183 4.9 51.1 1.0
OD1 B:ASP287 4.9 89.0 1.0

Manganese binding site 4 out of 8 in 6vrs

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Manganese binding site 4 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:89.7
occ:1.00
 OD2 B:ASP287 2.0 91.9 1.0
OE2 B:GLU181 2.1 0.0 1.0
OE1 B:GLU217 2.4 74.7 1.0
O B:HOH503 2.4 57.6 1.0
OD2 B:ASP245 2.4 83.3 1.0
O B:HOH501 2.6 66.5 1.0
CD B:GLU181 3.0 88.5 1.0
O B:HOH502 3.1 72.2 1.0
CG B:ASP287 3.2 84.3 1.0
OE1 B:GLU181 3.2 89.1 1.0
O B:HOH504 3.5 34.6 1.0
CD B:GLU217 3.6 73.4 1.0
CG B:ASP245 3.6 82.4 1.0
CB B:ASP287 3.8 72.8 1.0
CE1 B:HIS220 4.1 61.7 1.0
OD1 B:ASP287 4.2 89.0 1.0
MN B:MN401 4.2 88.0 1.0
CG B:GLU181 4.4 71.3 1.0
CB B:ASP245 4.4 73.9 1.0
OE2 B:GLU217 4.5 76.8 1.0
CG B:GLU217 4.5 65.6 1.0
OD1 B:ASP245 4.5 83.3 1.0
CB B:GLU217 4.6 56.6 1.0
NE2 B:HIS220 4.8 67.2 1.0
ND1 B:HIS220 4.9 53.6 1.0

Manganese binding site 5 out of 8 in 6vrs

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Manganese binding site 5 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:89.7
occ:1.00
 OD2 C:ASP287 2.0 91.9 1.0
OE2 C:GLU181 2.1 0.9 1.0
OE1 C:GLU217 2.4 74.5 1.0
O C:HOH503 2.4 57.8 1.0
OD2 C:ASP245 2.4 83.4 1.0
O C:HOH501 2.6 66.5 1.0
CD C:GLU181 3.0 88.3 1.0
O C:HOH502 3.1 72.7 1.0
CG C:ASP287 3.2 84.4 1.0
OE1 C:GLU181 3.2 89.0 1.0
O C:HOH504 3.5 34.5 1.0
CD C:GLU217 3.6 73.3 1.0
CG C:ASP245 3.6 82.3 1.0
CB C:ASP287 3.8 72.8 1.0
CE1 C:HIS220 4.1 62.1 1.0
OD1 C:ASP287 4.2 89.0 1.0
MN C:MN402 4.2 87.3 1.0
CG C:GLU181 4.4 71.1 1.0
CB C:ASP245 4.4 73.8 1.0
OE2 C:GLU217 4.5 76.4 1.0
CG C:GLU217 4.5 65.4 1.0
OD1 C:ASP245 4.5 83.3 1.0
CB C:GLU217 4.6 56.4 1.0
NE2 C:HIS220 4.7 67.5 1.0
ND1 C:HIS220 4.9 53.7 1.0

Manganese binding site 6 out of 8 in 6vrs

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Manganese binding site 6 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:87.3
occ:1.00
 OD2 C:ASP255 2.4 85.2 1.0
OE2 C:GLU217 2.4 76.4 1.0
NE2 C:HIS220 2.5 67.5 1.0
OD1 C:ASP257 2.6 83.2 1.0
OE1 C:GLU217 3.0 74.5 1.0
CD C:GLU217 3.1 73.3 1.0
OD1 C:ASP255 3.1 76.3 1.0
CG C:ASP255 3.1 76.4 1.0
OD2 C:ASP257 3.2 83.3 1.0
CE1 C:HIS220 3.3 62.1 1.0
CG C:ASP257 3.3 75.5 1.0
CD2 C:HIS220 3.6 63.7 1.0
OD2 C:ASP287 3.9 91.9 1.0
O C:HOH503 4.0 57.8 1.0
MN C:MN401 4.2 89.7 1.0
ND1 C:HIS220 4.4 53.7 1.0
ND2 C:ASN247 4.5 55.0 1.0
CG C:GLU217 4.6 65.4 1.0
CG C:ASP287 4.6 84.4 1.0
CG C:HIS220 4.6 57.6 1.0
CB C:ASP255 4.6 68.2 1.0
NZ C:LYS183 4.7 56.7 1.0
CB C:ASP257 4.8 65.8 1.0
CE C:LYS183 4.9 52.0 1.0
OD1 C:ASP287 4.9 89.0 1.0

Manganese binding site 7 out of 8 in 6vrs

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Manganese binding site 7 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:88.0
occ:1.00
 OD2 D:ASP255 2.4 84.1 1.0
OE2 D:GLU217 2.5 77.0 1.0
NE2 D:HIS220 2.5 66.0 1.0
OD1 D:ASP257 2.6 85.2 1.0
OE1 D:GLU217 3.0 71.1 1.0
CD D:GLU217 3.1 70.9 1.0
CG D:ASP255 3.1 76.5 1.0
OD1 D:ASP255 3.1 75.6 1.0
OD2 D:ASP257 3.2 89.7 1.0
CG D:ASP257 3.3 79.2 1.0
CE1 D:HIS220 3.3 61.5 1.0
CD2 D:HIS220 3.6 63.2 1.0
OD2 D:ASP287 3.9 89.7 1.0
O D:HOH503 3.9 51.0 1.0
MN D:MN402 4.3 91.8 1.0
ND1 D:HIS220 4.5 53.4 1.0
ND2 D:ASN247 4.5 54.0 1.0
CG D:ASP287 4.6 82.6 1.0
CB D:ASP255 4.6 66.1 1.0
CG D:GLU217 4.6 63.7 1.0
CG D:HIS220 4.6 57.6 1.0
NZ D:LYS183 4.7 57.1 1.0
CB D:ASP257 4.7 68.1 1.0
CE D:LYS183 4.8 50.5 1.0
OD1 D:ASP287 4.9 88.5 1.0

Manganese binding site 8 out of 8 in 6vrs

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Manganese binding site 8 out of 8 in the Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Single Particle Reconstruction of Glucose Isomerase From Streptomyces Rubiginosus Based on Data Acquired in the Presence of Substantial Aberrations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:91.8
occ:1.00
 OD2 D:ASP287 2.0 89.7 1.0
OE2 D:GLU181 2.1 0.5 1.0
OD2 D:ASP245 2.4 82.6 1.0
O D:HOH503 2.4 51.0 1.0
OE1 D:GLU217 2.4 71.1 1.0
O D:HOH502 2.5 80.6 1.0
CD D:GLU181 2.9 88.3 1.0
O D:HOH501 3.1 70.2 1.0
OE1 D:GLU181 3.2 91.2 1.0
CG D:ASP287 3.2 82.6 1.0
O D:HOH504 3.5 29.7 1.0
CG D:ASP245 3.6 80.6 1.0
CD D:GLU217 3.6 70.9 1.0
CB D:ASP287 3.9 72.0 1.0
CE1 D:HIS220 4.1 61.5 1.0
OD1 D:ASP287 4.2 88.5 1.0
MN D:MN401 4.3 88.0 1.0
CG D:GLU181 4.3 72.7 1.0
CB D:ASP245 4.4 72.5 1.0
OD1 D:ASP245 4.5 80.8 1.0
CG D:GLU217 4.5 63.7 1.0
OE2 D:GLU217 4.5 77.0 1.0
CB D:GLU217 4.6 54.1 1.0
NE2 D:HIS220 4.8 66.0 1.0
ND1 D:HIS220 4.9 53.4 1.0

Reference:

R.Bromberg, Y.Guo, D.Borek, Z.Otwinowski. High-Resolution Cryo-Em Reconstructions in the Presence of Substantial Aberrations Biorxiv V.Full 2020.
Page generated: Sun Oct 6 07:36:35 2024

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