Atomistry » Manganese » PDB 5z2k-6a9u » 5ze1
Atomistry »
  Manganese »
    PDB 5z2k-6a9u »
      5ze1 »

Manganese in PDB 5ze1: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C

Enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C

All present enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C:
2.3.2.27;

Protein crystallography data

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C, PDB code: 5ze1 was solved by M.S.Kim, W.Chuenchor, X.Chen, M.Gellert, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.68 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.760, 108.600, 157.090, 90.00, 114.20, 90.00
R / Rfree (%) 19.7 / 23.2

Other elements in 5ze1:

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C (pdb code 5ze1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C, PDB code: 5ze1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 1 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:68.6
occ:1.00
OD2 A:ASP600 2.0 57.0 1.0
OE1 A:GLU962 2.2 60.0 1.0
O3' F:DG30 2.2 75.2 1.0
OE2 A:GLU962 2.2 57.4 1.0
OP2 F:DT31 2.5 67.9 0.8
CD A:GLU962 2.6 57.7 1.0
CG A:ASP600 2.9 57.4 1.0
P F:DT31 2.9 70.5 0.8
OD1 A:ASP600 3.2 66.8 1.0
C3' F:DG30 3.5 59.2 1.0
MN A:MN2003 3.6 72.9 1.0
C4' F:DG30 3.8 50.1 1.0
O A:GLY601 3.8 57.3 1.0
ND2 A:ASN965 3.9 50.9 1.0
OP1 F:DT31 4.0 69.7 0.8
OP1 F:DG30 4.0 51.8 1.0
O5' F:DT31 4.1 81.8 0.8
CG A:GLU962 4.1 47.5 1.0
O A:HOH2104 4.1 74.7 1.0
C2' F:DG30 4.1 54.3 1.0
CB A:ASP600 4.3 57.9 1.0
O3' I:DA16 4.3 80.5 0.8
C5' F:DT31 4.4 84.3 0.8
C1' F:DG30 4.7 51.9 1.0
C5' F:DG30 4.7 52.9 1.0
O4' F:DG30 4.8 55.1 1.0
CE1 A:HIS795 5.0 59.3 1.0

Manganese binding site 2 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 2 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2003

b:72.9
occ:1.00
OD2 A:ASP708 2.0 69.9 1.0
OD1 A:ASP600 2.2 66.8 1.0
O3' I:DA16 2.2 80.5 0.8
O A:HOH2104 2.2 74.7 1.0
OP2 F:DT31 2.2 67.9 0.8
O I:HOH101 2.8 84.9 1.0
CG A:ASP708 3.2 65.6 1.0
CG A:ASP600 3.3 57.4 1.0
C3' I:DA16 3.6 84.8 0.8
MN A:MN2002 3.6 68.6 1.0
P F:DT31 3.7 70.5 0.8
OD2 A:ASP600 3.8 57.0 1.0
OD1 A:ASP708 4.0 72.4 1.0
C4' I:DA16 4.1 80.4 0.8
OE1 A:GLU662 4.2 73.7 1.0
CB A:ASP708 4.2 59.0 1.0
N A:GLY601 4.4 58.5 1.0
O A:GLY601 4.4 57.3 1.0
OE2 A:GLU662 4.4 80.7 1.0
OE1 A:GLU962 4.4 60.0 1.0
C2' I:DA16 4.4 88.3 0.8
OP1 F:DT31 4.4 69.7 0.8
O3' F:DG30 4.6 75.2 1.0
CB A:ASP600 4.6 57.9 1.0
O5' F:DT31 4.6 81.8 0.8
CD A:GLU662 4.7 70.5 1.0
C5' F:DT31 4.7 84.3 0.8
C5' I:DA16 4.8 76.3 0.8
CA A:ASP600 4.8 60.2 1.0
NE2 A:HIS795 4.9 67.4 1.0

Manganese binding site 3 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 3 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2002

b:73.3
occ:1.00
OD2 C:ASP708 1.9 71.2 1.0
O C:HOH2101 2.1 84.8 1.0
O C:HOH2106 2.3 63.4 1.0
O3' J:DA16 2.4 76.3 0.8
OD1 C:ASP600 2.4 68.6 1.0
OP2 G:DT42 2.7 68.7 0.8
CG C:ASP708 3.1 67.0 1.0
OD1 C:ASP708 3.6 67.0 1.0
CG C:ASP600 3.7 61.0 1.0
C3' J:DA16 3.7 82.3 0.8
OE1 C:GLU662 3.9 72.7 1.0
O5' G:DT42 3.9 76.0 0.8
P G:DT42 3.9 71.4 0.8
MN C:MN2003 4.0 65.2 1.0
OE2 C:GLU662 4.0 75.0 1.0
N C:GLY601 4.1 57.5 1.0
O C:GLY601 4.1 58.9 1.0
C4' J:DA16 4.3 82.7 0.8
CD C:GLU662 4.4 74.8 1.0
CB C:ASP708 4.5 53.8 1.0
OD2 C:ASP600 4.5 76.7 1.0
CB C:ASP600 4.6 53.9 1.0
C2' J:DA16 4.7 84.8 0.8
OE1 C:GLU962 4.7 58.0 1.0
CA C:ASP600 4.8 54.2 1.0
CA C:GLY601 4.8 57.8 1.0
C C:GLY601 4.9 55.0 1.0
OP1 G:DT42 4.9 69.1 0.8
C C:ASP600 4.9 55.7 1.0
O G:HOH103 5.0 58.3 1.0

Manganese binding site 4 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 4 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2003

b:65.2
occ:1.00
OE1 C:GLU962 2.1 58.0 1.0
OE2 C:GLU962 2.1 55.4 1.0
OD2 C:ASP600 2.2 76.7 1.0
OP2 G:DT42 2.3 68.7 0.8
O G:HOH103 2.3 58.3 1.0
O3' G:DG41 2.4 63.9 1.0
CD C:GLU962 2.4 49.5 1.0
CG C:ASP600 2.7 61.0 1.0
OD1 C:ASP600 2.8 68.6 1.0
P G:DT42 2.9 71.4 0.8
O C:HOH2106 3.6 63.4 1.0
C3' G:DG41 3.6 49.1 1.0
O5' G:DT42 3.7 76.0 0.8
O C:GLY601 3.8 58.9 1.0
MN C:MN2002 4.0 73.3 1.0
CG C:GLU962 4.0 47.7 1.0
C2' G:DG41 4.1 44.8 1.0
OP1 G:DT42 4.2 69.1 0.8
C4' G:DG41 4.2 49.3 1.0
CB C:ASP600 4.2 53.9 1.0
OD1 C:ASN965 4.3 56.5 1.0
C5' G:DT42 4.5 80.4 0.8
OD2 C:ASP708 4.6 71.2 1.0
O5' G:DG41 4.7 58.9 1.0
O3' J:DA16 4.7 76.3 0.8
OP1 G:DG41 4.8 62.9 1.0
C C:GLY601 4.9 55.0 1.0
C1' G:DG41 4.9 46.6 1.0

Reference:

M.S.Kim, W.Chuenchor, X.Chen, Y.Cui, X.Zhang, Z.H.Zhou, M.Gellert, W.Yang. Cracking the Dna Code For V(D)J Recombination Mol. Cell V. 70 358 2018.
ISSN: ISSN 1097-4164
PubMed: 29628308
DOI: 10.1016/J.MOLCEL.2018.03.008
Page generated: Tue Dec 15 04:49:50 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy