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Manganese in PDB 3t1i: Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations

Protein crystallography data

The structure of Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations, PDB code: 3t1i was solved by Y.B.Park, J.Chae, Y.Kim, Y.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.53 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.790, 135.210, 135.380, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations (pdb code 3t1i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations, PDB code: 3t1i:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3t1i

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Manganese binding site 1 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


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 Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:46.5
occ:1.00
 NE2 A:HIS22 2.2 56.9 1.0
OD2 A:ASP60 2.3 57.9 1.0
OD2 A:ASP20 2.3 67.3 1.0
NE2 A:HIS247 2.3 54.5 1.0
O A:HOH519 2.7 46.2 1.0
O A:HOH504 2.8 60.7 1.0
CG A:ASP20 3.1 54.2 1.0
CE1 A:HIS22 3.1 52.9 1.0
CG A:ASP60 3.1 54.5 1.0
CD2 A:HIS22 3.2 53.4 1.0
CD2 A:HIS247 3.2 56.9 1.0
CE1 A:HIS247 3.3 54.0 1.0
MN A:MN413 3.4 0.7 1.0
CB A:ASP20 3.4 46.7 1.0
CB A:ASP60 3.4 35.5 1.0
OD1 A:ASP20 4.1 54.3 1.0
O A:HIS245 4.1 52.3 1.0
ND1 A:HIS22 4.2 55.5 1.0
CA A:ASP20 4.3 53.8 1.0
CE1 A:HIS217 4.3 62.9 1.0
CG A:HIS22 4.3 53.8 1.0
OD1 A:ASP60 4.3 52.9 1.0
CG A:HIS247 4.3 57.5 1.0
ND1 A:HIS247 4.4 55.1 1.0
NE2 A:HIS217 4.6 71.8 1.0
OD1 A:ASN128 4.9 81.1 1.0
CA A:ASP60 4.9 38.2 1.0

Manganese binding site 2 out of 8 in 3t1i

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Manganese binding site 2 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


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 Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:0.7
occ:1.00
 NE2 A:HIS217 2.4 71.8 1.0
OD2 A:ASP60 2.4 57.9 1.0
ND1 A:HIS245 2.4 60.9 1.0
OD1 A:ASN128 2.5 81.1 1.0
ND2 A:ASN128 2.5 78.3 1.0
CG A:ASN128 2.8 66.6 1.0
O A:HOH519 2.9 46.2 1.0
CE1 A:HIS245 3.0 60.7 1.0
CE1 A:HIS217 3.1 62.9 1.0
CG A:ASP60 3.4 54.5 1.0
MN A:MN412 3.4 46.5 1.0
CD2 A:HIS217 3.4 58.0 1.0
CG A:HIS245 3.7 55.3 1.0
OD1 A:ASP60 3.7 52.9 1.0
OD2 A:ASP20 4.0 67.3 1.0
O A:HOH504 4.1 60.7 1.0
O A:HIS245 4.1 52.3 1.0
CB A:ASN128 4.2 36.2 1.0
NE2 A:HIS245 4.2 60.4 1.0
CB A:HIS245 4.2 59.0 1.0
ND1 A:HIS217 4.3 53.7 1.0
CA A:HIS245 4.3 60.6 1.0
N A:ASN128 4.3 58.6 1.0
CG A:HIS217 4.5 52.2 1.0
ND1 A:HIS129 4.5 62.7 1.0
CD2 A:HIS245 4.6 59.4 1.0
C A:HIS245 4.6 62.0 1.0
CB A:ASP60 4.7 35.5 1.0
CE1 A:HIS129 4.8 62.6 1.0
CA A:ASN128 4.9 54.6 1.0

Manganese binding site 3 out of 8 in 3t1i

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Manganese binding site 3 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


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 Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn412

b:56.5
occ:1.00
 NE2 B:HIS22 2.1 60.3 1.0
NE2 B:HIS247 2.2 58.8 1.0
OD2 B:ASP60 2.3 64.6 1.0
O B:HOH507 2.4 41.1 1.0
OD2 B:ASP20 2.5 68.1 1.0
CE1 B:HIS22 2.9 53.0 1.0
CD2 B:HIS247 3.2 53.6 1.0
O B:HOH509 3.2 58.3 1.0
CE1 B:HIS247 3.2 56.5 1.0
CD2 B:HIS22 3.2 53.5 1.0
CG B:ASP60 3.2 55.0 1.0
CG B:ASP20 3.3 56.1 1.0
MN B:MN413 3.4 99.6 1.0
CB B:ASP20 3.6 46.2 1.0
CB B:ASP60 3.6 38.9 1.0
ND1 B:HIS22 4.1 55.1 1.0
O B:HIS245 4.1 57.7 1.0
CG B:HIS22 4.3 52.5 1.0
ND1 B:HIS247 4.3 57.6 1.0
CG B:HIS247 4.3 61.7 1.0
OD1 B:ASP20 4.3 58.2 1.0
OD1 B:ASP60 4.4 52.4 1.0
CA B:ASP20 4.4 58.9 1.0
CE1 B:HIS217 4.5 62.4 1.0
NE2 B:HIS217 4.7 74.5 1.0
CD2 B:HIS129 4.9 57.6 1.0
NE2 B:HIS129 4.9 61.3 1.0
OD1 B:ASN128 4.9 79.4 1.0

Manganese binding site 4 out of 8 in 3t1i

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Manganese binding site 4 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


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 Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn413

b:99.6
occ:1.00
 NE2 B:HIS217 2.4 74.5 1.0
OD2 B:ASP60 2.4 64.6 1.0
ND1 B:HIS245 2.4 63.0 1.0
OD1 B:ASN128 2.5 79.4 1.0
ND2 B:ASN128 2.5 75.9 1.0
O B:HOH507 2.6 41.1 1.0
CG B:ASN128 2.8 63.8 1.0
CE1 B:HIS245 3.0 64.3 1.0
CE1 B:HIS217 3.2 62.4 1.0
MN B:MN412 3.4 56.5 1.0
CG B:ASP60 3.4 55.0 1.0
CD2 B:HIS217 3.4 61.2 1.0
CG B:HIS245 3.7 60.9 1.0
OD1 B:ASP60 3.7 52.4 1.0
OD2 B:ASP20 4.0 68.1 1.0
O B:HIS245 4.0 57.7 1.0
CB B:ASN128 4.2 35.7 1.0
O B:HOH509 4.2 58.3 1.0
CB B:HIS245 4.2 59.6 1.0
NE2 B:HIS245 4.2 66.0 1.0
CA B:HIS245 4.3 62.0 1.0
ND1 B:HIS217 4.3 57.3 1.0
N B:ASN128 4.4 59.7 1.0
CD2 B:HIS129 4.4 57.6 1.0
CG B:HIS217 4.5 56.2 1.0
CD2 B:HIS245 4.6 60.6 1.0
C B:HIS245 4.6 66.2 1.0
CB B:ASP60 4.7 38.9 1.0
NE2 B:HIS129 4.8 61.3 1.0
CA B:ASN128 4.9 56.2 1.0

Manganese binding site 5 out of 8 in 3t1i

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Manganese binding site 5 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn412

b:42.5
occ:1.00
 NE2 C:HIS247 2.2 51.1 1.0
NE2 C:HIS22 2.2 52.9 1.0
OD2 C:ASP60 2.3 53.7 1.0
OD2 C:ASP20 2.4 63.4 1.0
O C:HOH509 2.7 36.1 1.0
O C:HOH520 2.7 53.5 1.0
CE1 C:HIS22 3.0 52.1 1.0
CD2 C:HIS247 3.1 56.1 1.0
CG C:ASP20 3.2 54.0 1.0
CE1 C:HIS247 3.2 54.3 1.0
CG C:ASP60 3.3 49.9 1.0
CD2 C:HIS22 3.3 49.1 1.0
MN C:MN413 3.4 99.8 1.0
CB C:ASP20 3.5 49.5 1.0
CB C:ASP60 3.6 42.8 1.0
O C:HIS245 4.1 45.9 1.0
ND1 C:HIS22 4.2 54.2 1.0
CG C:HIS247 4.2 60.1 1.0
OD1 C:ASP20 4.3 57.6 1.0
ND1 C:HIS247 4.3 56.7 1.0
CG C:HIS22 4.4 53.6 1.0
OD1 C:ASP60 4.4 51.5 1.0
CE1 C:HIS217 4.5 63.0 1.0
CA C:ASP20 4.5 52.7 1.0
NE2 C:HIS217 4.7 67.3 1.0
OD1 C:ASN128 5.0 82.5 1.0
CD2 C:HIS129 5.0 55.5 1.0

Manganese binding site 6 out of 8 in 3t1i

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Manganese binding site 6 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn413

b:99.8
occ:1.00
 OD1 C:ASN128 2.4 82.5 1.0
NE2 C:HIS217 2.4 67.3 1.0
ND1 C:HIS245 2.4 60.7 1.0
OD2 C:ASP60 2.4 53.7 1.0
ND2 C:ASN128 2.5 74.5 1.0
CG C:ASN128 2.8 65.8 1.0
O C:HOH509 3.0 36.1 1.0
CE1 C:HIS245 3.0 58.4 1.0
CE1 C:HIS217 3.2 63.0 1.0
MN C:MN412 3.4 42.5 1.0
CG C:ASP60 3.4 49.9 1.0
CD2 C:HIS217 3.4 58.0 1.0
CG C:HIS245 3.7 58.0 1.0
OD1 C:ASP60 3.7 51.5 1.0
OD2 C:ASP20 4.0 63.4 1.0
O C:HIS245 4.0 45.9 1.0
CB C:ASN128 4.2 34.1 1.0
O C:HOH520 4.2 53.5 1.0
NE2 C:HIS245 4.2 59.1 1.0
CB C:HIS245 4.3 59.5 1.0
N C:ASN128 4.3 54.6 1.0
ND1 C:HIS217 4.3 53.6 1.0
CA C:HIS245 4.3 61.4 1.0
CD2 C:HIS129 4.4 55.5 1.0
CG C:HIS217 4.5 55.2 1.0
CD2 C:HIS245 4.6 62.4 1.0
C C:HIS245 4.6 60.0 1.0
CB C:ASP60 4.7 42.8 1.0
CA C:ASN128 4.9 52.5 1.0
NE2 C:HIS129 4.9 53.7 1.0
N C:HIS129 5.0 45.9 1.0

Manganese binding site 7 out of 8 in 3t1i

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Manganese binding site 7 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn412

b:58.4
occ:1.00
 NE2 D:HIS22 2.1 61.7 1.0
NE2 D:HIS247 2.3 65.0 1.0
OD2 D:ASP60 2.3 63.8 1.0
OD2 D:ASP20 2.5 65.0 1.0
O D:HOH504 2.5 44.3 1.0
O D:HOH508 2.9 64.5 1.0
CE1 D:HIS22 2.9 54.6 1.0
MN D:MN413 3.1 0.9 1.0
CD2 D:HIS22 3.2 57.9 1.0
CD2 D:HIS247 3.2 61.3 1.0
CG D:ASP20 3.2 63.2 1.0
CG D:ASP60 3.2 57.9 1.0
CE1 D:HIS247 3.2 59.0 1.0
CB D:ASP60 3.5 39.7 1.0
CB D:ASP20 3.5 50.2 1.0
ND1 D:HIS22 4.1 60.9 1.0
O D:HIS245 4.1 51.9 1.0
CG D:HIS22 4.3 57.2 1.0
OD1 D:ASP20 4.3 64.4 1.0
ND1 D:HIS247 4.3 63.2 1.0
CG D:HIS247 4.4 62.3 1.0
OD1 D:ASP60 4.4 55.6 1.0
CA D:ASP20 4.4 57.8 1.0
CE1 D:HIS217 4.5 66.4 1.0
NE2 D:HIS217 4.7 76.5 1.0
CD2 D:HIS129 4.9 57.6 1.0
NE2 D:HIS129 5.0 56.9 1.0
CA D:ASP60 5.0 44.5 1.0

Manganese binding site 8 out of 8 in 3t1i

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Manganese binding site 8 out of 8 in the Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn413

b:0.9
occ:1.00
 ND1 D:HIS245 2.4 58.5 1.0
NE2 D:HIS217 2.4 76.5 1.0
OD2 D:ASP60 2.4 63.8 1.0
ND2 D:ASN128 2.5 80.2 1.0
O D:HOH504 2.5 44.3 1.0
CE1 D:HIS217 3.0 66.4 1.0
CE1 D:HIS245 3.1 64.8 1.0
MN D:MN412 3.1 58.4 1.0
CG D:ASN128 3.3 66.8 1.0
CG D:ASP60 3.4 57.9 1.0
OD1 D:ASN128 3.5 81.6 1.0
CG D:HIS245 3.5 63.8 1.0
CD2 D:HIS217 3.5 62.3 1.0
OD2 D:ASP20 3.6 65.0 1.0
O D:HIS245 3.6 51.9 1.0
OD1 D:ASP60 3.9 55.6 1.0
CA D:HIS245 4.0 64.4 1.0
CB D:HIS245 4.0 61.8 1.0
O D:HOH508 4.1 64.5 1.0
C D:HIS245 4.2 64.6 1.0
ND1 D:HIS217 4.2 58.9 1.0
NE2 D:HIS245 4.2 67.0 1.0
CD2 D:HIS245 4.5 66.2 1.0
CG D:HIS217 4.5 53.6 1.0
CB D:ASP60 4.6 39.7 1.0
CB D:ASN128 4.7 38.0 1.0
CG D:ASP20 4.7 63.2 1.0
N D:ASN128 4.7 54.6 1.0
CD2 D:HIS129 4.7 57.6 1.0
NE2 D:HIS247 4.7 65.0 1.0
CD2 D:HIS247 5.0 61.3 1.0
NE2 D:HIS22 5.0 61.7 1.0

Reference:

Y.B.Park, J.Chae, Y.Kim, Y.Cho. Crystal Structure of Human MRE11: Understanding Tumorigenic Mutations Structure V. 19 1591 2011.
ISSN: ISSN 0969-2126
PubMed: 22078559
DOI: 10.1016/J.STR.2011.09.010
Page generated: Sat Oct 5 17:59:28 2024

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